Comment 4 by danconquer :

I don't think it's particularly helpful when atheists join in with the likes of the Taliban in denouncing moderate forces as somehow "not proper muslims", just as I wouldn't condemn catholics who use condoms as "not proper christians". Every incident, however small, when people use their intellect to rationally overcome supernaturalist dogma is good and we should always encourage it, not seek to alienate people who, whether we like it or not, are not yet ready to feel as though they are abandoning their religious community.

It is unreasonably judgmental to use the word "denouncing". Saying that "someone who doesn't follow everything in the Koran is not a proper Muslim" isn't a criticism from an atheist's point of view. It is a statement based on the nature of Islam.

If someone doesn't follow everything in the Koran, are they disagreeing with Allah, (Islam says the Koran is a recital via the Angel Gabriel of text created in heaven by Allah), or do they dispute the claim that the words are by Allah? (Or is there something else?)

Islam requires that the Koran is taken literally as the word of Allah in a way that Christianity doesn't claim the Bible is literally the word of God. The Koran (not Mohammad) is the way of accessing the word of Allah in the way that Jesus (not the Bible) was/is the way of accessing the word of God. Disputing the Koran is equivalent to disputing Jesus.

If we can't recognise that those people are not true Muslims according to Islam, we may have trouble seeing why there is a reaction against them, and why they may be afraid of people who do take things more literally.