As a hopefully religious person myself, I can sympathize with those who are offended by the desecration of their religious symbols. I would not purposefully do anything to disrespect any religion, and I think it is reasonable to expect others to do the same.
But three things strike me about the discredited Newsweek story saying that US soldiers flushed the Koran down the toilet, causing deadly riots in Afghanistan.
One is that the level of respect that Muslims demand of the Koran cross the line from reasonable requests into bigotry. Check out what US policy really is in Guantanamo on how to handle a Koran: