V for Vendetta is an excellent graphic novel, and the movie is also great.
However, the movie is presented in such a way that the viewer can interpret it as they wish. The Wachowski brothers, who wrote the script, love doing stuff like that. Upon viewing the film and their larger body of work, it becomes clear that they are students of philsophy who respect all religions (including Islam, as V for Vendetta, with scenes respecting the Quran and satirising the villification of Arabs and Muslims, shows).
How you choose to interpret their work politically though, is entirely your prerogative.
For what it's worth, Alan Moore and David Lloyd, the creators of the original graphic novel, meant for it to be a satire of Thatcher Britain, and a possible future extrapolated from such a political climate. Muslims weren't singled out in the graphic novel, though there were still scenes featuring concentration camps with all non-white people and homosexuals being hoarded in to be experimented on.