Sam Harris has found that detractors deliberately misrepresent his views:
It is impossible to effectively defend oneself against unethical critics. If nothing else, the law of entropy is on their side, because it will always be easier to make a mess than to clean it up. It is, for instance, easier to call a person a “racist,” a “bigot,” a “misogynist,” etc. than it is for one’s target to prove that he isn’t any of these things. In fact, the very act of defending himself against such accusations quickly becomes debasing. Whether or not the original charges can be made to stick, the victim immediately seems thin-skinned and overly concerned about his reputation. And, rebutted or not, the original charges will be repeated in blogs and comment threads, and many readers will assume that where there’s smoke, there must be fire.
Such defamation is made all the easier if one writes and speaks on extremely controversial topics and with a philosopher’s penchant for describing the corner cases—the ticking time bomb, the perfect weapon, the magic wand, the mind-reading machine, etc.—in search of conceptual clarity. It literally becomes child’s play to find quotations that make the author look morally suspect, even depraved.
He starts by describing his views on Islam:
My criticism of faith-based religion focuses on what I consider to be bad ideas, held for bad reasons, leading to bad behavior. Because I am concerned about the logical and behavioral consequences of specific beliefs, I do not treat all religions the same. Not all religious doctrines are mistaken to the same degree, intellectually or ethically, and it would be dishonest and ultimately dangerous to pretend otherwise. People in every tradition can be seen making the same errors, of course—e.g. relying on faith instead of evidence in matters of great personal and public concern—but the doctrines and authorities in which they place their faith run the gamut from the quaint to the psychopathic. For instance, a dogmatic belief in the spiritual and ethical necessity of complete nonviolence lies at the very core of Jainism, whereas an equally dogmatic commitment to using violence to defend one’s faith, both from within and without, is similarly central to the doctrine of Islam. These beliefs, though held for identical reasons (faith) and in varying degrees by individual practitioners of these religions, could not be more different. And this difference has consequences in the real world. (Let that be the first barrier to entry into this conversation: If you will not concede this point, you will not understand anything I say about Islam. Unfortunately, many of my most voluble critics cannot clear this bar—and no amount of quotation from the Koran, the hadith, the ravings of modern Islamists, or from the plaints of their victims, makes a bit of difference.)
You’ll need to read the whole thing.