Cuba’s Catholic Church is enjoying new popularity and influence — and TIME magazine examines why, and some of the challenges the Church is facing:

Last November, it opened a new seminary — the first since Fidel Castro’s communist revolution all but shut down the church 50 years ago. In May, Cuba’s bishops finished brokering the release of 115 political prisoners. Though education is strictly the role of the regime, Catholic dioceses have been able to expand their training of teachers, civic leaders and entrepreneurs — they even offer that iconic capitalist degree, the M.B.A. A statue of Cuba’s Catholic patroness, La Virgen de la Caridad (Our Lady of Charity), is being hailed by large, devoted crowds as it tours the island before her 400th anniversary next year. “It demonstrates a spiritual desire in Cubans,” Cardinal Jaime Ortega, Cuba’s top prelate, told me. It is, he adds, “a return to God.”

But any sense of exultation by church leaders is tempered by a familiar feeling of persecution. Its role in the prisoner releases has been questioned by critics who accuse the church of accepting the regime’s onerous condition that the freed dissidents go into exile. (Most did leave for Spain, but Ortega insists it was by choice and not part of any deal.) Conservative Cuban Americans like U.S. Representative Ileana Ros-Lehtinen, chairwoman of the House Foreign Affairs Committee, have branded Ortega a government “collaborator” because they feel he’s too quiet about human rights. Meanwhile, progovernment militants are harassing dissident groups like the Damas de Blanco (Ladies in White), prisoners’ wives and other relatives outside Catholic churches in the capital, Havana, and cities like Santiago.

The church is discovering that being the first — and only — alternative institution to the Cuban revolution is both a blessing and a curse. As President Raúl Castro, who took over for his ailing older brother Fidel in 2008, tries to engineer politically perilous economic reforms in his severely cash-strapped nation, he seems to have decided the church is the only noncommunist entity he can trust to aid those transitions without seriously challenging his rule. Speaking to the National Assembly in August, Raúl even offered a mea culpa for decades of blacklisting “Cubans with religious beliefs.” Says Ortega: “We’re breathing an atmosphere of change, feeling a moment when there are no more confrontations” between church and state.

But confrontation is exactly what many Castro critics crave. What good is the church’s return to the Cuban center stage, they ask, if it doesn’t spark democratic change, as the Polish church did a generation ago in Eastern Europe? The clergymen plead for patience. Miami Archbishop Thomas Wenski, who has aided the Cuban church’s revival, says his counterparts there are “opening new space for individual initiative and independent thought,” which they believe could help hasten communism’s demise when Fidel, 85, and Raúl, 80, die. But Ortega warns against the church “overreaching,” and Wenski says that it also wants to promote “a sense of reconciliation” among Cubans……

….The Jesuit-educated Fidel declared Cuba an atheist state in the 1960s: he banned Catholic media, expropriated church schools and exiled or hounded out 3,500 priests and nuns. Only 200 clerics remained to minister to millions of Cuban Catholics. The openly faithful, including priests like Ortega, were often sent to labor camps for “re-education.”

The church began to regain its footing in the 1980s, but its fortunes rose with the economy’s collapse in the 1990s, after the fall of Cuba’s benefactor, the Soviet Union. Sensing the usefulness of Catholic aid organizations like Caritas, whose Cuba chapter Ortega founded in 1991, Fidel proclaimed the island merely a “secular” state. Then, in 1998, he welcomed a historic visit by Pope John Paul II. The planning of that event, says Wenski, was a watershed: “It gave Catholics there a new confidence and planted the seeds of civil society.” That was evidenced by new Catholic publications like Vitral magazine, one of the island’s first independent media.