What you are not comprehending here is that you cannot separate the good Muslims from the bad Muslims in this manner. They cannot speak against or act against other Muslims.
Have you heard any Muslim leaders speak against Islamic Jihad against the West? Have they condemned the attacks and other atrocities committed by the terrorists?
Some have, but very few. And many of those have had their lives threatened for it.
When you have a billion people on "the other side," it only makes sense to try to draw lines that allow as many as possible of the enemy to switch sides gracefully. As I'm sure will begin to happen once the WOT really gets rolling again.
Which, unfortunately, will not happen until after another attack on this country.