If you aren't aware of the sheer volume of troubling and barbaric passages and teachings in the Quran then I really can't engage any further. Notable apologists like Reza Aslan, who is notorious for obfuscating his Islam arguments and insists that socio-economic issues are more to blame than religion (again, if you are unaware of how nefarious he is first read this: Reza Aslan is wrong about Islam are always bending over backwards to steer the argument away from the unavoidable shortcomings of the major religions.

Ben was more than just not-a-scholar that day. He was going head-to-head with essentially an authority on religious immorality and it's definitive effects on the world. Sam at no point "appealed to authority." Appealing to authority is the fallacy the religious commit on a daily basis; that because so many people believe it there must be some validity to it. What Sam was doing was referencing cold hard facts. Again, facts that are unpalatable but which are empirically proven and independently verifiable. And Affleck didn't want to hear it, nor did he have the sensibility to let Harris make his point and simply frowned and yelled over him while he tried to talk.

If a religion contains certain nuggets of wisdom, but is also full of archaic and useless doctrines that condemn people to punishment for essentially living their lives a way counter to their beliefs, it can still be considered a motherload of bad ideas. If 15% of an ideology believe that death to apostates or homosexuals is appropriate or that criticism of their religion can be met with violence, and that 15% amounts to dozens if not hundreds of millions of people, that is a major problem that clearly you, Ben Affleck and Reza Aslan would prefer to ignore until it's too late.