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First of all, I make no bones about the fact that I'm a pro-military, pro-war on terror and so forth.
But with that, the movie didn't bother me. The people who see it as an attack on the Bush administration (though it IS mentioned in the film in passing while showing anti-war protests), are seeing it as such because they WANT to see it as such.
Yeah there are if not veiled, then outright insults at Conservatism (odd how I see the main villian in the movie being more in line with the Left than the Right, yet I'm sure the opposite is true for the Sheehanites and their ilk), but overall it was still enjoyable.
The use of real riot footage was actually well done (though my thoughts on the rioters in the real world are less than kind) and fit the purpose of the movie, so I had no problem with them in the picture.
The problem with bringing forward a political statement from either side is that from the left you have to accept that your view of the Bush administration is one of cariacature and not based in any way on actual reality, and from the right, that those on the left can convince others that the administration is the cariacature they are portraying.
All in all you have to accept it for what it is... fiction that shows the issues of dealing with extremism, which exists on both sides of the aisle
Personally, I think that the extreme left DOES see the Bush admin like the villian in the movie, however I see the movie for the fiction that it is, so in that regards, it doesn't bother me.
The movie was enjoyable and can be watched without the pre-conception that it is an attack on Conservatives, Bush, the Right, et al.