Listen, I'm not a fan of Maher but that video was mostly him bashing religion, specifically Islam. Maher is not kind to any religion, but he especially hates Islam give it's repressive attitude towards women and homosexuals as well as the violence it tends to inspire. You can dance around it all you like but Islam, at the moment, is the most violent and repressive religion. Yes, some lone Christian nut might blow up an abortion clinic or shoot up a school. Yes Catholic priests we know didlly dally with little kids. And yes, the Church has certain restrictive views when it comes to birth control. But, nothing with regards to other religions are close to the scale of consistent violence and repression found in Islam in our current global society.
Saudi Arabia as a country exists. UAE as a country exists. Yemen. Syria. Qatar. Etc. These are all countries that enforce Islam to a strict degree and are among the worst human rights abusers on the planet. It's understandable that Maher, a smug Atheist, finds such a religious practice despicable. He doesn't really deny that moderate Muslims exist it's the notion that the majority of Muslims in the world are totally tolerant that he disagrees with, because as he sees it the evidence is clear that they are not. Take Maher to task for Milo walking over him, but his arguments against Islam are not out of nowhere.