Eteraz points out that Islam is not the same thing as Islamism and backs this up by noting that there are voices within Islam that argue against Islamist interpretations of the faith:-
[The] thing that Sam Harris doesn't quite understand is that even the most outspoken voices against Muslim fanaticism do draw a line between Islam and Islamism. Tarek Fatah, whose book against the Caliphate I previously reviewed on Cif, was featured in a documentary whose very title refutes Harris: "Islam v Islamists". In other words, there is a distinction between the two concepts and it is adhered to by the kind of people Harris claims he's looking for. No wonder he can't find them.Theological distinctions between various strands of Islamic thought are obviously important and it's true that Harris's scatter gun approach tends to elide such distinctions. Nevertheless, Eteraz misunderstands Harris if he thinks that demonstrating a clear distinction between the two will somehow lead Harris to stop criticizing Islam. Harris is an outspoken atheist, he is opposed to religion per se - specifically, he regards religious dogma as an obstacle to spritual and ethical progress.
In many ways, Harris makes the same mistake the fundamentalist Muslims do, which is to believe that self-critical Muslims are not as sincere about their faith as the fundamentalists and therefore they do not represent the "real" religion. This is the basic fallacy that prevents him from realising that the Islam that self-critical Muslims adhere to is, at the end of the day, Islam.
Personally, I'm not immediately troubled by what people believe, or say they believe; I'm more interested in people's actions. If someone threatens me, it's the threat that bothers me not the belief system behind it. Nevertheless, I don't see a problem with criticizing religious doctrine (I've done it myself, on occasion) and I can't accept the claim (made by one of the bloggers Eteraz cites in support of his views) that criticism of religion has no part in "responsible civil discourse".
I rather think that appeals to religious authority have no part in reasonable discourse and I particularly resent being told that I should accept the authority of religious figures when it comes to what I can and can't speak about.