the movie was basically all about how the terrorists and the American government were the same for what they do. You hear it when the terrorists are speaking to each other about America and when the Government is talking about the terrorists. You see it when Cheadle accuses Jeff Daniels for being no better than 'them'. You see it when Cheadle tells the FBI, "the only difference is that the other guy knows he's an asshole." Throughout the whole movie all these parallels are drawn between the terrorists and American government. That is what I also took from the last scene of the movie. The government cleared his file basically telling him what you said "all your crimes are overlooked because you did one good thing." They thought just like the terrorists. That paralleled the scene when they were talking about chess and how you have to sacrifice some of your pawns. Both the terrorists and government think like that. Cheadle didNOT think like. But someone below said there was no part in the movie where Cheadle changed and I don't think that is true. I think he changed in the scene where he told his girl she had to forget about him. He still believed what he believed but he also knew that he was in too deep at that point. And when Jeff Daniels told him "all of the people would have dies in vain if they stopped" he knows he is right but he still tells Jeff he is just like the terrorists because he is the only one that sees what is going on. But like I said, he was in too deep at that point and knew what he needed to do.
As far as the people all going on one bus, I actually liked that part because it brought the movie full circle. Cheadle finally realized he had to sacrifice. And judging by people's responses, everyone thought that he would've given them bombs that didn't work so they didn't take the predictable route.
Another thing about the last scene, it also showed how it is never going to stop because the FBI then tried to recruit Cheadle to help them, which in essence would be the same thing he was doing for the terrorists. Both the government and terrorists just 'use' people and that was the main point of the entire movie. How both groups were very much alike.