In a communitarian vision, not only individuals have rights; so do families and institutions, including religious institutions. Pope Benedict XVI, speaking to a group of American bishops last January, found it necessary for the first time in American history to speak about threats to religious liberty in the United States. He said: "At the heart of every culture, whether perceived or not, is a consensus about the nature of reality and the moral good, and thus about the conditions for human flourishing ... The church has a critical role to play in countering cultural currents which, on the basis of an extreme individualism, seek to promote notions of freedom detached from moral truth."
I think this is badly phrased. Only individuals can have "rights," because only individuals can have responsibilities. A person who thinks a group can have responsibilities should try standing in the kitchen with 11 other people and saying, "These dishes need to be washed." The dishes will be washed by the individual who is too proud to be an idle drone. For a different example, who goes to jail if a crime is committed? Not an institution, but an individual.
Freedom of conscience and free exercise of religion are rights that adhere to individuals. The liberty of institutions, including churches, is based on the free-association and free-exercise rights of each individual member of the group.
It would be nice if we could say that the Church, as the Body of Christ, has a functional "personhood" in such a way that it can be the subject of rights, but in the absence of a realistic way to collectivize responsibility, we need to be *very* careful about speaking of anything but individual rights.