"But the holy book's many references to "disbelievers" and the violent punishments they should suffer aren't directed specifically toward atheists, says Mustafa Abu Sway, dean of the College of Islamic Studies at Al-Quds University. Because atheism wasn't a big issue when the Koran was written, mentions of "disbelievers" in the book are actually references to polytheists, people who worship idols, or occasionally to followers of other monotheistic religions like Judaism and Christianity, says Abu Sway"

Further evidence that the Quran is not a perfect, universal and timeless guide for all humanity, but rather a culturally/historically relative document intended for 7th century Arabs.

Why the general hatred and violence for non-muslims, particularly polytheists? A people who were quite tolerant and accepting of all religions, up until Muhammad's constant derogatory comments concerning Arab polytheism, which inflamed tensions with the Meccan Arab polytheists. Why inflict violence on peaceful disbelief? Is Islam that insecure and flawed, it requires coercion and intimidation to thrive? What a false, flawed and antiquated superstition.

"What's more, that violence was only permitted in self-defense"

'History is written by the victors'. Coming from a Muslim apologist, I'll take that with a pinch of salt. It is well known Muhammad and the early Muslims conducted offensive missions and caravan raids.

Moreover how is,"kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush.", covered by "self-defence"?

Is the above verse also historically relative to 7th century Arabia?

"Such nuances, however, may be lost on the average Muslim living in Najaf or Maan. Koranic verses are often misconstrued or—worse—taken out of context, wielded to suit the whims of the individual."

A book that proclaims itself to be 'perfect', would not lead to so much misinterpretation. (To so much conflicting, contradicting and competing interpretations- some violent, some peaceful- many self-proclaiming as 'True Islam') hardly a 'perfect' and 'clear' religion.