This argument is something that crops up to a greater or lesser degree whenever any of Scientology's flagship supporters make a movie, most notably when Travolta had his pet project to shoot L Ron Hubbard's Battlefield Earth some years ago.
Having read that book (which it's true is no Tale of Two Cities, but nevertheless quite a decent page-turner), I found myself disagreeing with many who were slamming the book and the subsequent movie as rubbish (many of whom had never troubled themselves to read read the book or see the movie and thus form a true opinion). It was clear many critics of the book and movie had an agenda where Scientology was concerned and channelled that vitriol into their criticisms of the book, and particularly the movie. Both of which are nowhere near as bad as is popularly touted, but are tarred with that opinion largely because of many critics' inherent dislike for Scientology.
I, and I imagine most other people, do not base what movies they choose to watch on whether the actors and producers vote the same way as me, unless of course their movie is trying to ram their ideology down my throat. If he was doing a remake of Jude Suss or something, I think we might have an argument.
Now, I am not even remotely in favour of Scientology, but I nevertheless thought that to use one's dislike of it to slam something else was rather a cheap shot. Back on the subject of Tom's latest 'masterpiece', it's apparent that the same methods are being used to forestall its production, and whilst I personally am quite amused to see people making life hard for Tom Cruise, I do think that confusing one issue with another in order to prevent filming is not really easy to condone if you believe in freedom of expression.
At the end of the day, I would place my faith in the fact that it's likely to be a turkey of massive proportions if TC is involved in it, thus allowing him to fall on his own sword, rather than being pushed onto it by misguided censorship.
Chock