I think you and Aslan are right, you can't say "all", but I do think it is a valid question to ask "how many are hostile towards X?". Not just Islam, but other religions as well. How many Muslims in Turkey feel about X, despite it being a secular country? Here in the States our main issues involving religious extremism and anti-secularism happen to be mainly from Christian sources. Things like anti-stem cell, harassing and committing violence towards pro-choice institutions and laws, anti-gay rhetoric, christian-first rhetoric and so on. I think it's a valid question and inquiry to wonder how many people are out there like that. They need to be pointed out as much as possible because they are actively trying to chip away at secularism. I do think Maher has a small valid point, which is at times some progressives in this country are very hard on Christian influence and morality, but absolutely do make a point to go out of their way to be tolerant to Islam's belief system (for whatever reason that may be). Frankly, a lot of issues progressives have with Christian theology and morality can be found in Judaism and Islam, as well as other religions. Blasting one of them and tip-toeing around the others seems disingenuous (which Maher does with Judaism and Zionism all the time).
Secularism in itself involves separation of faith and state (in different degrees depending on the state), but at times it's much more complicated than even that. Some of the Scandinavian countries still have official state religions (Christianity) despite some of world's most hardline secular culture, laws and populations. You have countries like Israel where it is billed as secular and non-religious despite a very clear religious undertone to the very existence of the state, the symbolism in all of its entirety, preferential laws and Zionism in general. So at times it isn't purely a "secular vs theocratic" thing either because it often falls strictly on unique population sets within those jurisdictions.
I just felt my only minor point against what Aslan said was that he kind of dismissed the religious source of some of these issues nonchalantly.