I only have a vague, mostly second-hand idea of Sam Harris; but, I agree that he differs from Objectivists in pretty fundamental ways. Indeed, a decade ago, most Objectivists who point out his good bits would probably have focused on his bad bits. I think the reason is that one picks one's battles: and, I assume more Objectivists who listen to Harris, link to him, etc. would also acknowledge his flaws.
Analogously, the defeat of the Soviets in Afghanistan took the west from fighting an enemy whose philosophy was based on explicit naturalism and reason (the commies ) to an enemy with a mystical belief in the "uncreated" nature of an ancient scripture.
