Nicholas Kristof in the New York Times:
Whether or not Islam itself inspires conflict, debates about it certainly do. Our conversation degenerated into something close to a shouting match and went viral on the web. Maher and a guest, Sam Harris, argued that Islam is dangerous yet gets a pass from politically correct liberals, while the actor Ben Affleck denounced their comments as “gross” and “racist.” I sided with Affleck.
After the show ended, we panelists continued to wrangle on the topic for another hour with the cameras off. Maher ignited a debate that is rippling onward, so let me offer three points of nuance.
First, historically, Islam was not particularly intolerant, and it initially elevated the status of women. Anybody looking at the history even of the 20th century would not single out Islam as the bloodthirsty religion; it was Christian/Nazi/Communist Europe and Buddhist/Taoist/Hindu/atheist Asia that set records for mass slaughter.
Likewise, it is true that the Quran has passages hailing violence, but so does the Bible, which recounts God ordering genocides, such as the one against the Amalekites.
More here.