Read other letters about this article
I think that most people get uncomfortable with the idea that people can kill and murder and commit the most monstrous atrocities in the name of an ideology. As Ms Zacharek points out - the film does not shy away from addressing this point that these people were motivated completely by their religion. The Khafirs (non-believers) that they killed had no right to live, so the hijackers committed no sin. They were acting perfectly logically from their world view point.
The uncomfortable truth for a lot of people is the realization that no amount of reasoning, discussion or persuasion is going to change this viewpoint. No protest, no "sensitivity training", no good intentions will make a difference in their behavior. And because they are now moving about in our world, we cannot ignore them any more.
The passengers on Flight 93 took action to take the plane back after they realized this point. When they realized what the hijackers were intending - suicide bombs- the rules (and the world) changed. If the movie says nothing else - it shows that resistance in the face of this "truth" is not futile.