[TheDon]

I doubt that religion has anything to do with the reason for not allowing the movie to be filmed at the requested locations.

[Titus Quinctius Cincinnatus]

It was explicitly the stated reason (now, it may not have been the real reason, however....

Defense Ministry spokesman Harald Kammerbauer said the film makers "will not be allowed to film at German military sites if Count Stauffenberg is played by Tom Cruise, who has publicly professed to being a member of the Scientology cult".