HAVANA — Just in the past few days, with a visit here by Pope Benedict XVI looming, the Rev. Roberto Betancourt has witnessed firsthand the difficult position Cuba’s Roman Catholic Church finds itself in as it wields its newfound influence but still struggles to fill its pews....

Benedict faces an odd paradox in what is the first visit by a pope since John Paul II’s in 1998. The church’s profile as an institution has risen sharply in recent years amid a burst of religious tolerance not seen since the 1959 revolution, with church leaders advocating for political and economic freedoms, negotiating the release of dozens of political prisoners in 2010 and counseling the government on plans for re-engineering the economy.

At the same time, the church has struggled to attract more worshipers and faces criticism that it has grown too cozy with Cuba’s tight circle of decision makers....