V blows up the parliament because it doesn't exist in the world of the movie. He blows up a structure, which is unecessary because of the lack of an actual parliament. In my opinion, anyway.
There is no Church bad message in the film. There are two characters, a priest and a talk show host who both seem to discuss religion and are bad guys. But these guys specifically affected V in person--he's not against them based on their religious beliefs, nor does he care about anyone else in the priest hood period. He is also against a certain doctor. I can say personally that doctors, as a group (or undoubtedly, any individuals) feel that this film is a commentary about the evil of doctors. These people are individuals who personally acted against him (V). I'd love to elaborate more, but for fear of hurting the film, I shall not.
There is NO connection to current politics, period. Saying that it could be applied to current politics by the director says nothing about Bush or any other famous politician. I mean, on some amorphous level, any film that talks about politics could be connected to current politics. We could claim Shakespearian plays are about current politics with this line of reasoning. (really)
But this is too much. People are projecting imagery into a great film. Not everyone is out to get Bush (although a lot are). However, if Bush DID do the same stuff the characters in this film did, you'd be against him. Of course, he didn't, but I digress.
I don't think anyone that actually sees the film will come away feeling like it's any kind of commentary on current politics.
If the writer of the comic didn't like the movie, you should take that as a sign he has poor taste in films. Don't take it as anything else.
Even great comic book authors aren't guaranteed to appreciate great movies.