Islam came from a region that is fucked.
I don't honestly care about what Islam's message is (because I don't believe in it, since I don't agree with it - but that doesn't mean it needs to be wiped out or censored), or what a bunch of white guys from the Bible Belt think Islam's message is.
My opinion is to let them be - good, bad, whatever.
However, our greed has us deeply embedded in the Middle East. We want oil. We don't want to be liberators. We don't want to spread democracy. We don't want to spread peace, harmony, stability or any form of equality through out the Middle East.
As such, we've done things that have pissed the Muslims off. Their reaction is not justified. But, it is what it is. There is no turning back - and, no need to apologize frankly.
But, we continue to piss them off, because of greed.
If the Middle East was 'contained' (left as is - I am not talking about putting up walls), they would eventually sort things out and Muslims would direct their anger towards the real enemy; their leadership - government, ruling party AND religion.
Could you imagine what the Middle East would be like if the US and Israel wasn't involved in that region? Their streets would be littered with dead princes, dead dictators and dead Islamic extremists.
Our involvement has done one thing - aside from making a few people very rich - provided the ME' governments, ruling parties and extremist religious leadership a scapegoat.
Where do we go from here?
Get off of oil.
Let's drop all the bullshit about providing freedom as well as this whole 'eco-kook' stigma of getting off of oil and move away from that region.
To answer the OP's question: there isn't anything wrong with the vast majority of Muslims. What is wrong is that we've placed ourselves in a position to sway more and more peaceful Muslims into the extremists side. Each bomb we drop and kill an innocent, we sway 100 to 200 more Muslims to the extremists side.
And, bullshit counter-arguments about how collateral damage is the fault of the terrorists (because they are hiding in hospitals, using human shields, etc.) just adds more fuel to the hate towards as well as proves our indifference.
Now, there is no way in hell we can, or ever will, repair the damage done. But, we can move away from them and never look back. Let them figure it out, because our intentions, attitude and actual actions are just making things far far worse.