Where did this idea come from? Well, Newsweek makes the claim (without attribution). The Pentagon has been scrambling all over this, and has been unable to substantiate the actions alleged. In fact, Gen. Myers, Chair of the JCOS, says, the allegation that a Koran was flushed down a toilet seems to come from what a prisoner did -- attempting to stop up a toilet with pages from the Koran to make trouble for the guards.
Well, two things need to be said about this. One is, if anybody did indeed mistreat somebody's holy book as part of interrogation or psy ops or something, then that's wrong. We shouldn't be doing such things, and the doers thereof need to be punished, and the doing stopped immediately and henceforth. Of course, nobody's proved that we have done such things yet, and that's not a vain point.
The other thing that needs to be said -- politically incorrect as it might be -- is, what kind of lunatics are these Muslims who will kill each other and shout that they are ready to blow themselves up to get at the people who abuse their religious book? I mean, if someone abused the Bible, I'd be sore. I'd want someone punished, and an apology -- and certainly a policy stated explicitly that we don't abuse religious symbols and won't tolerate those who do. But rioting? Killing people? Screaming that I want to blow myself up to avenge the insult to my holy book?
Some people think that Islam is stuck in a time warp, and is in a schizoid state between the medieval and the modern. Maybe. But I try to understand the more violent emotional outpourings of the Islamic world by reference to medieval Christendom, and I don't find many comparisons. Maybe in the anti-Semitism of both cultures/time periods. But in some ways, Islam is simply unique. I can't come up with sufficient examples of Christian or Jewish or Hindu craziness to balance against the lunacy launched on a mere rumor over and over in the Islamic world. Is it the religion that has made them nuts? Or are their societies nuts, and it shows up in religious ways? Well, since Islam covers several major ethnic groups/states with varying histories, I'd have to say there's something in Islam or Islamic culture which is very, very disturbing.