And Islam, but his problem is more with its tenets and leadership than the people themselves.
Though he's often lumped into the "atheist" category (and has even referred to himself as one a few times), he's actually dissed militant atheism, saying it's just another form of certitude. Basically, unless you're a hard agnostic, your views are not safe from him!
He doesn't like Mormonism or Scientology either. He once went so far as holding an un-baptizing of the dead father-in-law of Mitt Romney, Edward Davies.
However, Mormonism got a Pet the Dog moment when polling pointed out that the one usually reliable Republican demographic that rejected Donald Trump in the 2016 election to any measurable degree were Mormons. Needless to say, Maher does not like Trump, so the situation also fits Enemy Mine to a certain degree.
Confirmation Bias: Maher attempts to subvert this, but generally if you agree with him you will like it, if you disagree with him you will hate it.
Critical Research Failure: Defended South Park for being against religion, when the creators of South Park are not against religion. Really his defense was of South Park's right to free speech, especially when the groups they target (in this case, Viacom under political pressure) are offended by it, despite the fact that the SP creators disagree with him on a lot of issues. He's made the same argument towards Rush Limbaugh, saying that he'd rather live in a country where people are allowed to say things that may offend others, than one where no one has the right to say anything that might rub against the grain.
Don't Shoot the Message: Many liberals and atheists dislike him both for his sexist comments and anti-vaccination statements.
Family-Unfriendly Aesop: Bill doesn't think adultery is that big a deal, as he's discussed adultery scandals from French politics.
Foe Yay: It's rumored he used to date Ann Coulter. He certainly has her on his show a lot.
From the May 8th, 2009 episode: "New Rule: The Supreme Court is a deliberative body, not a sausage party. We need a court that looks like America, not like a hundred-year reunion of the Whiffenpoofs. That's why Obama needs to find a non-lawyer, single parent with disabilities who is also a bi-curious black woman. [slide of Michael Jackson] Michael Jackson, your comeback starts now!" He died a month later.
In February 2016, he complained about the Supreme Court of the United States striking down an EPA rule, and asked how anything can be done in America if it 'has to be run by Antonin Scalia first.' Literally that night, Scalia died. The week right after that, he mentioned Nancy Reagan, and she died the next day. On the third week, he admitted that something spooky was going on with his show, and then namedropped Dick Cheney.
Heartwarming in Hindsight: In April 2011, Bill delivered the New Rule "Charlie Don't Serf", in which he urged Americans to stand up to the corporations who have been abusing the American socioeconomic system. In September that same year, the first Occupy Wall Street rally took place, which managed to influence American politics, coining terms like "The 1%", and has made people pay more attention to the increasing disparity between rich and poor people.
Hilarious in Hindsight: In the last show of his halfway point in the 2013 season, Bill remarked that "I get why Republicans don't want to come on my show, but I couldn't get Obama when he was a senator, Biden won't come on, Pelosi won't. Am I just the pot-smoking potty-mouthed talk show host to most Democrats?" Nancy Pelosi was his very first guest when the show came back from break (supposedly she saw said line and asked to come on). He didn't get the Obama visit until late 2016, at the tail end of Obama's presidency.
The Scrappy: One of Bill's most frequent guests, Stephen Moore, is widely hated for being seen as a near-cartoonish conservative strawman. And yet he's one of Bill's closer friends. Funny how that works.