Remember that this whole thread started with Kyrel's statement that the "vast majority" (which would be a lot more than a simple majority) of American Muslims are guilty of actions that should get them arrested, jailed, executed, or deported. I think this expresses a wrongful, destructive attitude which has continued to influence this thread, and that is what I am primarily arguing against.
I am also arguing that, whatever may be going on with Islam in more backward parts of the world, the vast majority of American Muslims are much the same as the vast majority of American Christians, and that if one goes looking for reasons to condemn a religion, there is not that much difference between Islam and Christianity.
There are a lot more Christians than Nazis in the United States, and it is much more reasonable to view a person with suspicion for self-identifying as a Nazi than to view them with suspicion for self-identifying as a Muslim or Christian.
Organizations like ISIS and Al-Qaeda are very serious problems that badly need to be dealt with, but our focus should be on those organizations, not on the whole religion.
There are two problems relevant to this discussion. On is the problem of ISIS and Al-Qaeda, which I agree is serious and spoke to just now. The other is the problem of general cultural and philosophical conditions in the world, which contribute to a lot of bad things happening. If we want to look for an arch villain in the latter, the best target is probably Immanuel Kant, who undercut reason and gave the altruist morality a new lease on life, thus strengthening religion and other misguided ideas and making possible a lot of bad things, including Naziism and the strength of religious fundamentalism. But our primary focus here should be on spreading good ideas, not attacking bad ones.