The best way for me to understand the Muslim uproar over the Koran burning and the Muhammed cartoons is to think of it in terms of desecration of the Eucharist (which, sadly, still happens nowadays). The desecrator might claim he's simply abusing a cracker, but Catholics understand that the cracker is actually Christ himself.
Granted, if I'm not mistaken, the Koran is a lot lower on the totem pole of sacredness for Muslims than the Eucharist is for Catholics (for Catholics, it doesn't get much higher).
Regardless, does (or should) the fact that a cultural or religious group holds something to be sacred give it any special protection in our society? Is intentionally desecrating this sacred thing considered a hate crime, and if not, should it be?
In a larger sense, if you do something that a person or group perceives as hurtful, and you are aware of this perception, but you don't think that any harm is actually done, are you in the wrong?