History of Roman Catholicism in Cuba
Cuban independence 
At the end of the 19th century, many Cubans viewed the Catholic Church as one of the primary enemies of the fledgling nation. There were two main reasons for this. The first had to do with the bond between Church and Crown. In exchange for the services that it provided the monarchy, the colonial Church received numerous privileges and exceptions. Priests were immune from prosecution in civil court, church buildings were erected and clergy members were paid partly out of state coffers. The Church's authority was backed by the might of the state and the force of law, and the profession of other religions in the colonies was illegal. Furthermore, until the 1880s, there was no marriage other than the canonical.
Many Cuban separatists believed the dominant position of the Church in the colonial era to be evidence of the backwardness of the Spanish monarchy. Similarly, others viewed any lingering privileges that might be accorded the Church after independence as a vestige of the injustices of the colonial period.
A more immediate reason for anti-clericalism being a component of Cuban nationalism was the fact that the Catholic hierarchy had actively sided with the Spanish monarchy against the Cuban revolutionaries during the armed conflict of 1868-1898.
Another major issue of contention was the fact that the Catholic Church of Cuba had failed to develop and sustain a significant native-born clergy. Many of the lower-ranking priests and all of the Catholic prelates were born in Spain. This led many Cubans to conclude that the primary allegiance of these men was to Spain, even before Rome.
The conflicts between Church and State during the first decades of the republic--e.g. over marriage, divorce, baptism, burial, education and the citizenship of priests--were in large part, direct attempts by Cuban nationalists to strike a blow against the Church, and to divest it of power and influence that they believed it held illegitimately.
Fidel Castro 
After the 1959 revolution, Cuba officially embraced atheism. Practicing Catholics and other believers were viewed with suspicion and discriminated against. Fidel Castro succeeded in reducing the Church's ability to work by deporting the archbishop and 150 Spanish priests, discriminating against Catholics in public life and education and refusing to accept them as members of the Communist Party. The subsequent flight of 300,000 people from the island also helped to diminish the Church there.
In 1992, Cuba declared itself a secular state and permitted Catholics and others to join the Communist Party. However, religious schools have remained closed since the early 1960s.
- Chadwick, A History of Christianity (1995), p. 266