It's a semantic disagreement, and neither of them understand that.
What is Islam? Who defines Islam?
Affleck chooses to define Islam as a religion of peace and equality, accepting the definitions of the liberal muslims (who are in the vast minority). It's a definition based in part on wishful thinking, but it may also be held with the knowledge that sometimes words carry more weight than their meanings, and it's not always impossible to change how these things are interpreted with the right voice. I think Affleck probably finds it more useful to define Islam the way he wishes it was, because if enough people do that the conservatives will be considered aberrant and Islam will be able to liberalize without losing its identity.
Harris chooses to allow the majority of Muslims, and conservative tradition, define what Islam is. To him, Islam is what the Hadith says it is. And Islam is what the majority of Muslims say it is- those Muslims who don't agree with that are only nominally Muslim, and don't really believe in their own faith. This is both very descriptive and technically correct in a lot of ways, but I'm not sure if he considers how useful it is, since it threatens the identity of those nominal Muslims and grants the extremists the cherished recognition of being Muslims.
Sam Harris wrote:And they do not realize that these doctrines are about as controversial under Islam as the resurrection of Jesus is under Christianity.
And not all people who identify as Christians believe that. The problem is that these terms are not owned or even very clearly defined, but are matters of identity for a lot of people regardless of what they believe.
It's just as
prescriptively accurate, and maybe more useful, to say that anybody who believes in the resurrection superstition isn't a Christian, but a Paulist.
Why? Because most Christians are going around and saying their small group are the only Christians anyway.
Conflating personal identity with ideology, and belief, and politics... it makes a big mess. And much of the argument over the matter comes down to how you define the groups, and make sense of these words - do you do it based on the majority, marginalizing exceptions, or do you just define them however you want and see who can shout louder?