sure, your points are for the most part valid. I'll disagree about the brief history of atheism, and point you to the writings of Epicurus, Spinoza and Hume... But more to the point, Reza's castigation of Maher and Harris seems to hinge on what he feels is a blanket condemnation of the Islamic faith, akin to the "Islamophobic" pseudo-racist label, which is frankly defensive and dishonest. Yet, when asked to distance himself from the half (or however much) of Islamic thought and scripture that espouses violence he won't do it- he says instead something about having to consider scripture in its entirety. Would he step up and suggest that there are pieces of Islamic scripture that are incorrect, that should be ignored? realizing the implication is clearly that if one accepts scripture to be flawed, one implies rejection of the claim that scripture is the infallible word of one's chosen deity and the whole religious house of cards is at risk.
Harris and Maher may have put a word wrong here and there- who hasn't- but the main message they seem to favor is that there are statements and ideas in all of the faiths that may have reflected the bronze age society in which they were written but that are immoral, illegal and proven incorrect now- and Islam may harbor the higher proportion of believers who espouse (or don't question) these immoral concepts, under the premise that the Quran is the word of Allah and must never be challenged.
I don't think Reza can dispute that point, so he tries to undercut the message by quote mining? He was pretty negative about Ayaan Hirsi Ali as well.