Islam is my least favourite religion. Has been, even before 9/11. It's a very problematic religion; it hasn't gotten a grip on its most extreme elements, it does the most harm to its believers (physically and mentally), and its adherents are, in general, the least tolerant of any religion I know. Its size and influence only serve to magnify the difficulty.
But I always felt uncomfortable about Islam-bashing, not because it was disrespectful of others' beliefs (they have to be true to earn my respect). The discomfort was this: take a walk around the seedier right-wing hate sites like Redstate or Malkin, and you'll see Islam-bashing in spades. So if I'm saying something against Islam, what's the difference between the right-wing haterz and me? Might I not be mistaken for the racists I despise? Even good ol' Christopher Hitchens, when he gets going on the danger of Islam, seems to blend in with the racists on the right. And it's taken him to some horrifying conclusions: the invasion of Iraq, and some saber-rattling on Iran. Even Ayaan Hirsi Ali, whose anti-Islam cred is impeccable, isn't usually mentioned with Dawkins or Harris, and I think it's because the Left feels uncomfortable with her since she sits so comfortably with the anti-immigration nutbars in the Dutch right-wing. And so my criticism of Islam, if I were inclined to make any, has been muted.
Only recently have I been able to see a crucial distinction that would resolve this conflict. It's the difference between religion and ethnicity. I'll oppose the religion of Islam — by means of reason, science, and education — because it teaches absurdities, and it's dangerous. I'll oppose every other religion on earth for the same reason. I'm an equal opportunity opposer. But when it comes to Arabs, Indonesians, Africans, or any other ethnicity, I have nothing to say.
When I was a kid, there were lots of Iranian uni students in my hometown. This was at the height of the Iranian hostage crisis in 1979. Listening to the Charlie Daniels Band on AM radio does something to a kid, and some of those Iranians seemed pretty scary. Scarier than normal uni students, which is pretty scary anyway. Fortunately, I had a wise father who took me to some cultural events on campus and got me to meet the students. (He liked the lamb.) I came to realise that even though Iran had just gone crazy, there was a segment of Iran that was secular and moderate, and who hated the new government. Understanding the difference between religion and ethnicity could have helped me a bit.
In connection with this, I'd also like to echo the sentiments of Dave at exchristian.net, who feels that while opposing religion is fair game, being horrible to actual people sucks. I now feel embarrassed when I think about the believer I used to be. Some are okay people, I was not. I knew the truth, dontcha know, and Jesus was my homeboy. I was good at getting around objections to the one true faith, and I must have been an intolerable pain. Fortunately I reformed and learned to question my received wisdom without fearing the wrath of hypothetical beings. Maybe someone in a religion now might be a future unbeliever. No need to be horrible to my future friend. I'll point out bad reasoning, but I hope I'll spare the messenger. Just in case I can learn something from them.