Well, there is no need to give another history lesson, so I will just repeat: you two are putting way too much emphasis on Islam and not enough on the political and social enviornmets US foreign policy has created.
If tapes and letters from bin Laden, bombers, etc dont make it clear on what they are responding to then I dont know what else to say. The US is not looked at so disfavorably in the region - and around the world - because of their religious views. It is largely the policies that breed the religious extremism. How many studies and opinion polls or communiques do you two need to be able to see this?
The reason I mentioned the Iranian example is because it is very instructive. You might also want to look into Nasser and secular nationalism in the region. It was strong in the 50s and 60s but went on the decline when US policies shifted to supporting oppressive governments that suppressed political rights, etc. And, not without surprise, religious extremism increased in its place.
Anyway, accept it or deny it. The truth of it all does not rely on our recognition.