While watching V for Vendetta with a protestant family member (after having watched it many times myself), I immediately had to defend the movie as not specifically being anti-protestant (or pro-catholic). But, as the movie went on, I wondered about this more and more, and didn't want to defend it unjustly.
The main points are I think (all of this is arguable; some of it may be incorrect/misinformation but is what I've been told):
historically, Guy Fawkes is specifically anti-protestant/pro-catholic, and the movie treats him positively
the rhyme "Remember, remember, the 5th of November" is turned around by the movie not to mean "beware of the (catholic) treason", but to mean to remember the catholic assassination attempt as a good thing, even something to be reenacted
the people that V kills are presented as either stereotypically protestant or at least stereotypically Anglican (as far as I know there is little difference)
V leaves Scarlet Carsons for many of his victims, which are symbols of the Catholic Church.
I think that's it, so it's not a strong case by any means, but it's something I can't stop wondering about. I would love to be able to say that the movie is more or less religiously and politically neutral (aside from of course being anti-authoritarian and pro-freedom).