I almost agree with Mr. Harris’ editorial with this particular exception:
“While the scriptures of Judaism and Christianity also contain terrible passages, it has been many centuries since they truly informed the mainstream faith.”
Not at all convinced that’s true.
I think the key word there is “mainstream.” We have Christian Reconstructionists who want to impose the Christian analog of sharia on the U.S. And we have Orthodox Jews, like Jonathan Rosenblum, who reject Mendelssohn and go all the way back to Maimonides, to the Middle Ages, for what they insist on defining as the cutting edge of Jewish thought (http://fora.tv/2007/07/26/Is_Darwinism_Kosher#chapter_03). But they’re not really mainstream in the same way.
In a broad sense I more or less agree with you, but I think there is an appealing tendency to slip into a sort of relativism. That relativism justifies categorizing any unique criticism of Islam as “bigotry,” although that’s obviously not what you’re doing. The irony is that the religious camps do this interchangeably. When one criticizes Christian fundamentalists, they whine, “why don’t you ever hear any criticism from liberals about Islam?” Good point. But when you criticize Islam, many liberals complain that you’re picking on a minority, saying, “why don’t you go pick on Christianity or Judaism?” It’s a neat trick.