As for the reasons Al Qaeda attacked us, you may want to investigate that further. Many who do bad things use a religuous undertone. Hitler blessed planes, for example. The Klan is heavily steeped in relgious rhetoric. But, their goals and actions are less religous then they are motivated by other goals. I suggest this is just as true with Al Qaeda. bad people speak religion, but seldom if ever actually represent the religion. So the enemy here is not the religion, but those like Al Qaeda who use the rhetoric for other purposes.
But at the end of the day, the flaw in the logic of those opposing the building is still that they see all Muslims as Al Qaeda, and that is no more accurate than seeing all Christians as the Klan, or as nazis, or any other group that has done evil in the world.