There was a very interesting segment on Democracy Now! about this story. Amy Goodman interviews two of the men involved. While it is just one side of the story, it is pretty darn compelling. I think this was fear and paranoia in action.
I do understand that fear and paranoia may be high on airplanes right now. The major injustice that US Airways committed was to not fly these guys after the FBI had cleared them after 5 hours of interviewing them. I do blame the paranoid passengers, too, though. I think people incorrectly equate terrorism with Islam. As usual, I am surprised that atheists like me are the ones standing up for these guys. You know the crazy left, all obsessed with civil liberties and shit.