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.
Broken Base: Many of Maher's fans heavily criticized his decision to have infamous troll and alt-right poster boy Milo Yiannopoulos as his interview guest for his February 17th, 2017 show, saying that it gave him a national platform to spout 'racist, transphobic, and homophobic' views. Other fans defended his decision, saying that liberals looked like cowards if they refused to challenge opposing views. Maher himself said that 'sunlight was the best disinfectant,' and indeed, it wasn't until after Milo attracted scrutiny from the mainstream media that they found a rather incriminating interview of his that resulted in him resigning from Breitbart News.
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.
Don't Shoot the Message: Many liberals and atheists dislike him both for his sexist comments and anti-vaccination statements.
Double Standard: Meshed with Karma Houdini during the February 17, 2017 episode involving New Rule segment, "The Magic R" as Maher discusses why Republicans have "Patriotic Immunity" and disputes the notion that they inherently love America more than Democrats.
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. Two weeks after that, he mentioned Nancy Reagan, and she died two days later. 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.