As far as I’m concerned, Sam Harris and his critics have the same problem. He’s saying that Islam is inherently violent; they’re saying it’s a peaceful religion which has been hijacked. Neither is true. Islam can’t be characterized as monolithically intolerant or benign, anymore than Christianity or Buddhism can.
The reason why Muslims haven’t been able to shed the jihad isn’t because their scriptures won’t allow them to — people can and do blatantly ignore and distort their traditions to justify whatever they want — but because real-world dynamics haven’t facilitated such a move. With the right impetus, the Islamic nations can do exactly what Europe did after 500 years of crusading — regardless of what the Qur’an says in this and that passage.
It’s true that the ratio of intolerance to benevolence in the Qur’an is rather high. But the ratio of pacifism to militancy in the New Testament is also high — and that didn’t stop a five-century crusading movement. It just doesn’t matter what one’s scriptures say. It’s getting the jihadists to want better things that’s the problem. I’ll have more to say about this in an upcoming review of Robert Spencer’s Politically Incorrect Guide to Islam and the Crusades, which makes arguments similar to those of Harris.