It has occurred to me that regardless of one's thoughts about Islam specifically, there is something strange in the liberal conviction that all religions can be "domesticated" to be liberal-friendly. One underlying current of all the talk about "Islamophobia" is the idea that "true Islam" is perfetly compatible with liberalism because in the end, all religion is the same, except for the extremists.
People who make the claim that all religious beliefs are the same, or that they all say pretty much the same thing, actually reveal that they have no respect for religion at all. In the end, they believe in secualr humanism, believe that it is so obvious that secular humanism is correct that everyone, deep down, really believes in that (or at least all people of goodwill), and that all religions ultimately boil down to secular humanism, and that what the official doctrines say really don't matter.
In short, most people who worry about "Islamophobia" do not take religion seriously (not just that they disbelieve the doctrines, they reject the notion that those doctrines have any real importance to those who believe in them), and therefore the concept that religious beliefs can be dangerous (as opposed to only extremists on any belief being dangerous) is foreign to them.
In the end, a lot of people assume that people of faith are no different than, e.g., Star Trek convention-goers, and therefore that differences in religious doctrine, rather than representing different beliefs about objective reality, are nothing more significant than opinions over whether or not the tie-in novels should be considered canon.
That is all.