Would you describe Sufism as theocracy-promoting? Or secular Islam? The fact is that there is a huge amount of diversity within was particular Muslims believe and to try to paint large groups of people with broad strokes just leads to gross inaccuracy. If you use this overgeneralization to justify prejudice... well people have used bad information to justify prejudice for a long time. We usually call them fundamentalists (fundamentalist christians, fundamentalist muslims, etc)
I'm an agnostic myself, but I appreciate diversity of thought and viewpoints that can exist in the world, and being prejudiced is not acceptable. I do agree that we should oppose intolerance. Ie if a particular Muslim (or group of Muslims), or the Militia, or the KKK, or the Westboro Baptist Church is preaching intolerance and trying to spread a message of hate, we should oppose that message. The people who get drawn into these ranks are likely stupid victims themselves, getting hoodwinked because of a need not being met by society (lack of opportunity, proper education, etc).
Religions are like assholes, and everyones got one whether it's scientific research, reading Emerson and Thoreau, gambling and drinking, or participating in a Church (or whatever intentionally religious) community. Most people ascribe to more than one religion and it's all fine. It's only a problem when they teach prejudice, intolerance and hate. As long as we can respect the first amendment, there is no problem here.