They had the balls to make a terrorist the hero. This is something I wouldn't advocate in real life, but anyone who is upset by that is missing the simple fact that it's a movie: It's a lurid, exaggerated, dramatic piece of fiction.
Think, though about the narrative of the movie. A conservative government controls the population with the one two combo of religion and fear. The fear is of terrorism, but the horrible terrorist acts that have allowed the government to take away civil liberties, were in fact created by that same government, in collusion with large corporations. Along the way they've created the man who will be their own undoing, a real terrorist.
The overly literal will wonder if they're saying that the government is behind terrorist acts like 9/11, and fulminate with righteous rage about it. But think about it. Both in the case of Saddam Hussein and Osama Bin Laden, their careers started by being lavishly bankrolled by the United States government. I'd be willing to bet they both were cordially engaged with the CIA right up until they did something that threatened US interests. Hussein invaded Kuwait, after getting mixed messages from American diplomats about how the US would react. Bin Laden attacked the US, repeatedly, not that long after the Taliban had been greeted as heros in the Reagan White House.
The main bullet point of the movie is "The people should not be afraid of the government, the government should be afraid of the people." is entirely relevant right now. We're at a point where nearly two thirds of the US opposes the occupation of Iraq, and there's no significant peace movement! Unlike most of you I'm old enough to remember demonstrations against the Vietnam War shutting down universities and even Washington DC. It's high time this happened again.
A wonderful detail in "V for Vendetta" is when "Street Fighting Man" by the Rolling Stones plays over the credits. This came out in 1968. On college campuses in the US when the students called a strike, people would put their speakers in the windows of the dorms and blast this song. Maybe that seems silly now, but for anyone who remembers 1968, its a song that's a big fat signifier perfectly tuned to the end of the film.