The problem isn't the religion... It's the fact that nearly all muslim nations are theocratic, making sure that they will never secularize their morality (like the united states and most european nations have). It wasn't too long ago that white people were brutalizing each other and burning witches at the stake or putting them on the rack for "bad" ideas. But, a few hundred years of philosophy later, the governments have secularized and our common morality has FAR surpassed the very strict religious codes that are actually IN the holy books themselves. Eventually, even the religious people stop listening to the brutal/horrible parts of their own books, sans maybe a few Phelps types.
In time, Islamic nations will chill out and start to look much more like Christianity is today. Most Muslims in the United States are kinda like this already, and wouldn't hurt anybody in the name of their religion.