I'm not exactly sure how it works, but i know in movies, people have to pay fees for usage of private buildings, like the C.N. Tower here in Canada. The CN Tower is a private building, contrary to most people's assumptions, so anyone making a movie with shots of the CN Tower have to pay a company that handles private building usage (which in turn pays the CN tower and other private buildings) for it's usage.

Whether a church is a private or public building, I'm not sure. And whether buildings are allowed to decline usage, I'm not sure about either.