First things first. Not Muslims. Extremists and unhappy, manipulated people that happen to be Muslims along the way. Catholics burned US flags too. Plenty of people dislike your nation and States aren't without a blame.
Back in the times of Cold War it was America and Soviet Russia that pumped millions into Afghanistan, supporting local crime lords. Both those nations armed the today's suicide bombers and terrorists, but back then it was 'right thing to do'. Cold War ended, and everyone left the middle east to it's own problems, leaving only tons of weapons behind. Neither of those 'super powers' spent money on eduction, infrastructure or humanitarian help along the way, creating a perfect environment of poverty for an extremist uprising.
Also.
Books are not to be burned. Never, ever. We've seen it already. Inquisition burned the 'forbidden' books, Nazi's burned books, do we want to uphold those 'noble' traditions? Furthermore, Koran is a religious book. Destroying it wouldn't show your disdain for the extremists, it would show your ignorance and lack of tolerance for different beliefs. Majority of Muslims doesn't go around blowing themselves up, why do you wan't to act against them? Further more, there is enough of catholic extremists that do similar things.
And finally, flag of USA is not a religious symbol. No matter how much brainwashing you wish to take. It's a symbol of government and national pride. Nothing more. So yeah, the backlash was deserved and thank god it happened. Last thing the world needs is escalation based on idiotic religious prejudice.