Nobody cared when Bill Maher (and Sam Harris) spent the last 15 years tearing christianity apart, but apparantly critizing a religion even more deserving of scrutiny and it's diehard adherents makes them the worst people in the world. They're simply concerned and they have a right to be concerned. Even more importantly, if you refuse to listen and denounce them as bigots, it only further empowers the truly bad people on the far right because like it or not, the islamic fundamentalist issue isn't going away and if sane, reasonable people on the left aren't allowed to dicuss it, the people will go (and have gone) to the only people who will and that's the real concern.
I would like to add however that Bill Maher slightly disappointed me on the trans issue. If he was informed at all then he would've refuted Milo's fake and misleading sexual abuse statistic and not referred to them as weirdos, but i'm still not going to throw him under the bus because of that unfortunate slip up.