After the various Dominican constitutions became successively more secular, the Vatican checked this evolution through a concordat. In 1954 the dictator Trujillo granted the Church privileges in return for Vatican recognition of his murderous regime. The dictator is now gone but, despite protests, the concordat remains.
Vatican aimed to freeze church-state relations and forstall patronato privileges over the Church
In 1844 "La Dominicana" won its independence from Haiti. The Dominican Republic's constitution of the same year regulated relations between church and state, in line with the national motto: "Dios, Patria, Libertad" ("God, Fatherland, Liberty").
However, by 1907 "the various Dominican constitutions [by then 14 in number] had evolved from establishing the Catholic religion as the state religion to including religious tolerance".  This constitutional development was made possible by the country's lack of a concordat. Without the constraint of a treaty with the Vatican, church-state relations were frequently adjusted by the Dominican parliament and moved towards secular values, including tolerance of other religions. The concordat was meant to end this evolution by freezing church-state relations in a form that met with Vatican approval.Actually, the Dominican Government had long wanted a concordat, in the mistaken assumption that this would confirm the new nation's control over its largest social institution. As former subjects of the King of Spain, they expected to inherit the powers which he had exercised over the national church. This privilege of "His Most Catholic Majesty" — which was extended to his colonial administration — was called the right of royal patronage (patronato real). It had been assumed as a matter of course by the newly independent countries of Latin America under the suitably republican name of "national patronage" (patronato nacional). However, the Vatican had no intention of granting to a small Caribbean republic the same concessions that it had conceded to the powerful King of Spain. The concordats of the various Latin American republics were meant to end, once and for all, the Spanish tradition of these states regulating their own national churches.
From the very beginning of the Dominican Republic conflict had flared up over who was to run the country. During a famous altercation in 1853, the country's first president, General Pedro Santana, informed the Archbishop of Santo Domingo, Monsignor Tomas de Portes e Infante:
The president is resolved to see that these laws are enforced, that the courts observe and uphold them. ...The people must provide laws for themselves and cannot tolerate two powers in the State ....
To this the Archbishop replied:
I do not pledge allegiance to wicked laws.... There are two powers here, the civil and the Church.
Only under threat of expulsion from the new republic, did Archbishop Portes finally pledge allegiance to the new constitution and the laws of the republic. 
In March 1884 an unofficial agreement with the Vatican (sometimes called a "convention" or "modus vivendi") was signed in Rome. This secured for the Church whatever privileges could be got, until a formal and more comprehensive concordat could be worked out. This provisional agreement ended the open conflict by obliging the churchmen to formally acknowledge the constitution:
[It] provided that the Catholic religion was the state religion but that other religions were allowed in their respective temples. [...] It was also stipulated that all ecclesiastical authorities should swear allegiance to the Dominican constitution before occupying their positions. 
It was, however, a coup for the Vatican because it did away with the traditional patronato which would have given the government the right to name the country's Catholic bishops, as well as veto power over appointments of clergy down to the parish priest level.  Instead, it stipulated that
the archbishop of Santo Domingo [was] to be appointed by the Pope from a list of three names, native Dominicans or residents of the Republic, submitted by the Dominican Congress, which in turn engaged to pay the salary of the archbishop and certain other officials. 
The Concordat with Trujillo, "Benefactor of the Church"
It wasn't until well into the 20th century that the time was ripe for a favourable concordat. As Hitler, Franco, Salazar, Duvalier and many others found, when a dictator needs Church support, the price for this is often a concordat. So it was with Generalissimo Rafel Trujillo, the de facto ruler of the Dominican Republic from 1930 until his assassination in 1961. Nicknamed "Bottlecaps" (Chapitas) for his fondness for medals, he also liked embroidered uniforms, epaulettes and hats with ostrich plumes. However, life under Trujillo was no comic opera.
By the 1950s Trujillo had a number of reasons to want recognition by the Vatican.
♦ The Generalissimo had become an international pariah, as the world learned of "The Cutting" ("El Corte"), the 1937 slaughter with machetes of thousands of Haitians living in the Dominican Republic  and of the torture and/or murder of everyone who opposed him. His assassination attempt on the President of Venezuela didn't come until 1960, but even by 1954 Trujillo was so scorned internationally that Vatican recognition in the form of a concordat was a welcome prospect.
♦ This diplomatic alliance with the Vatican would also help Trujillo consolidate his anti-Communist credentials. On 6 March 1953 the Dominican Republic became the first Latin American state to sign a mutual defence pact with the US — several months before Fidel Castro's first abortive attempt to launch a revolution in Cuba that June.  Trujillo, the "medal-jingling" dictator on the island next to Cuba, savoured his new importance as Defender of the Free World against Godless Communism.
♦ And naturally, the support of the Church would help Trujillo domestically, as well. If the Catholicism of some of his countrymen was not entirely orthodox, it was nonetheless enthusiastic. In fact the emphasis of Dominican religion on health cures let Trujillo insert himself into the colourful local pantheon of saints, folk healers (curanderos) and witches (brujos). "Only Trujillo cures you," said the inscription on a hospital. Public fountains proclaimed "Trujillo gives water".  Hundreds of towns, streets, buildings were renamed after Trujillo, his father, his mother, and his patron saint, Rafael.  His political slogan was "God and Trujillo". Dominican schoolchildren recited daily prayers for "God, country, and Trujillo".  And a Church bull of 1935 talks of "the political-Catholic genius of the distinguished magistrate Generalissimo and Doctor Don Rafael Leonidas Trujillo Molina, whom his compatriots [...] have honoured with the golden laurels of Benefactor of the Church and Father of the New Fatherland."
The 1954 concordat
Generalissimo Franco had signed a concordat in 1953 and the next year Generalissimo Trujillo followed suit.
Relations between the Catholic Church and the dictator Rafael Leonidas Trujillo (Trujillo) were very good at the beginning. [...] By 1931 Trujillo granted legal status to the Catholic Church, besides building many churches, seminaries, schools and institutions which were run by nuns and priests brought from Spain. 
Through the 1954 concordat the Church obtained control over marriage and religious instruction and frustrated Trujillo's attempts to claim for himself the presentation of bishops, (patronato real), the privilege of Spanish kings.
With the signing of the concordat great benefits were granted to the Catholic Church [for example, access to public funds and exemption from import duties]. It allowed the creation of dioceses, and bishoprics were established in Santiago and the Vega. Until then there had been only one hierarchy in the country which was the Archbishopric of Santo Domingo. Religious instruction was also established in public schools. Religious marriage was made official and divorce was prohibited between those who had been married by the Church. Other religions were at a disadvantage compared with the Catholic and one of them, Jehovah’s Witnesses, was banned by a 1957 law, due in reality to the members’ refusal to enlist for mandatory military service."
Protests against Trujillo's concordat
On 11 July 2006 representatives of the Dominican Republic's more than 1,600 Protestant churches filed an appeal against this concordat with the Dominican Supreme Court (SCJ). They claimed that it is unconstitutional. However, over two years later on 22 October 2008 the Supreme Court upheld the concordat. In its ruling
it states that although the State assumes the obligation to teach the Catholic religion and moral education in elementary and secondary public schools, in no way prohibits that education by another religion in their establishments, nor has evidence been contributed that demonstrates that this has been prevented by virtue of what is agreed to in the Concordat. 
The Protestant group has said that this ruling violates human rights and that it will consider taking this before an international body. The powerful Cardinal Lopez immediately replied that, no, it doesn't, and that anyway the concordat is strictly a matter between the State and the Holy See. 
Then, a few weeks later (the day before the signing of the Brazilian concordat) he voiced what has become the Vatican argument: “Don't fight it, join it”. He advised the Protestant groups to get their own church-state agreements. 
Whether they will try to do so, as the Protestant church in Germany has, remains to be seen. One group, however, has stated clearly that it is not interested in sharing the privileges, but intends to go on fighting for their abolition. The Masons, who uphold church-state separation, have been petitioning Congress for years, appealing for the establishment of “a secular state, totally independent of all religious influences, in order to guarantee before the state the absolute equality of all its citizens who profess different beliefs”. They also asked that “the role of the State be limited to maintaining and respecting the rights to freedom of conscience and of religion of each and every one of our citizens, without any distinctions, preferences or privileges.” 
1. Juan Francisco Puello Herrera, "Religious Freedom, the Church and the Dominican State", p. 7. Presented 3 October 2005, at the Twelfth Annual International Law and Religion Symposium, 2-5 October 2005, Brigham Young University, Provo, Utah. http://www.iclrs.org/symposium/2005/papers/Puello%20Herrera%20Paper%20-%20English.pdf
2. Herrera, ibid., p. 4.
3. Herrera, ibid., p. 6.
4. The arrangement secured the year before by Franco in his concordat.
“Spain: A country study”, [under “Society --> Religion”], Area Handbook Series. 2d edition. Edited by Eric Solsten and Sandra W. Meditz. Prepared by Library of Congress, Federal Research Division. Research completed Dec. 1988. http://countrystudies.us/spain/44.htm
5. Otto Schoenrich, Santo Domingo: A Country With A Future, 10th Edition, 1918. http://www.gutenberg.org/etext/9813Schoenrich
[In 1697, Hispaniola was divided, what is now Haiti, being ceded to France as "Saint-Domingue" and the Spanish remnant, what is now the Dominican Republic, was called "Santo Domingo" -- hence title of this book.]
6. “The massacre that marked Haiti-Dominican Republic ties”, BBC News, 13 October 2012. http://www.bbc.com/news/world-latin-america-19880967
7. Social Sciences and Humanities Library, University of California San Diego,
"Dominican Republic: Elections and Events 1945-1962". http://sshl.ucsd.edu/collections/las/dominicanrepublic/1945.html
8. "EI Benefactor", Time, 30 July 1951. http://www.time.com/time/magazine/article/0,9171,815155-1,00.html
9. "Case Study: Trujillo and the Dominican Republic", 26 November 2006. [A conscientiously researched class paper by a blogger named Lisane.]
10. "Rafael Leónidas Trujillo", Wikipedia. http://en.wikipedia.org/wiki/Rafael_Le%C3%B3nidas_Trujillo
11. "EI Benefactor", ibid.
12. Salesian Bull, 11 October 1935, cited in Carlos Nouel, Historia eclesiástica de la Arquidiócesis de Santo Domingo, (Rome 1913 and Santo Domingo 1914), III, 388.
13. Herrera, ibid., p. 7.
14. Herrera, ibid., p. 8.
15. “Landmark ruling upholds Vatican-Dominican State pact”, Dominican Today, 23 October 2008. http://www.dominicantoday.com/dr/local/2008/10/23/29833/Landmark-ruling-upholds-Vatican-Dominican-State-pact
16. “El cardenal dominicano critica a los protestantes por rechazar el concordato” (“The Cardinal criticises Protestants for rejecting the concordat”), Soitu.es, 24 October 2008.
17. “Cardenal pide otras iglesias firmen pactos con Estado”, (“The Cardinal invites the other churches to make pacts with the State”), 12 November 2008. [reposted without attribution on a Catholic site about the beliefs of cardinals] http://www.cardinalrating.com/cardinal_50__article.htm
18. “The Masons again demand nixing Dominican-Vatican pact”, Dominican Today, 22 February 2007 http://www.dominicantoday.com/app/article.aspx?id=22646 The full quotes are found in the press release of 21 February 2007, “Masones reclaman Estado laico y anulación del Concordato”, (“The Masons appeal for a secular state and the annulment of the Concordat”). http://elmason.blogspot.com/2007/02/masones-reclaman-estado-laico-y.html