I'm not quite as outraged as the OP, but I do think the political over-analysis is a bit much. If you really want to see those things in the movie, you can find plenty of tidbits to support your thesis. But having the conclusion first and looking for the evidence later is not the way to go about things.

The movie makes valid, significant points about the nature of terror, morality, crime, and even the human condition, I think. But you lose the well-crafted subtleties by looking for references to Bush and 9/11.