I did not know the Holy Quran has a verse: 'Slay the pagans wherever you find them, seize them, beleaguer them, lie in wait for them with every stratagem.' (Quran 9:5)., although I read quite a lot on happenings in the Islamic world. If taken out of context (even if taken in context, I guess) this statement looks unambiguous.
Mr. Beg could not bring himself to condemn violence unequivocally in what would otherwise have been a nice article on outright condemnation of violence on innocents. The title 'Islam does not sanction violence' should have dwelt just on that. Citing the issues of injustice to Muslims in the same article shows Mr. Beg has succumbed to the 'root cause' effect that he so elaborately mentions. All this 'root cause' thing could have come in a different article.