Robert Wright's post in the NY Times today was an interesting read. I think he is right about Pipes's view, it's characterized by cognitive dissonance. We can't win the war on terrorism in a military sense without a coherent entity to be eliminated by force. Military action is properly conceived of as conflict between states, transferring the same logic onto other forms of conflict doesn't make any sense and simply leads to lots of tough sounding nonsensical metaphors.
However, I don't think Wright's view is correct either. While the rhetoric of conflict is being used and it no doubt helps recruiting we were getting attacked sporadically before major US military intervention. Trying to link all of this back to the overthough of Mossadeq or intervention in Afghanistan is quite a stretch and mistaking justifications for root causes.
Of course people look for a cause because there was a time we weren't under threat from this direction. The mistake being made is thinking that the change has to do with our own actions rather than what happened abroad. There was a brief period when the developed world was mostly isolated from anyone with a different culture, except through colonial exploitation. As technology improved and travel became easier increased contact occurred at all levels which, in addition to the benefits, led to violence. This is a historical constant. Lots of good things come with contact but there is also always a little bit of violence along the fringes, fringes which now reach every part of our country due to air travel. This isn't mean to endorse the clash of civilizations view point, I'm talking about low level conflict that marked most cross-cultural borders, not broad civilization wide conflict which is more of an exception.
In this specific case, you have a culture still steeped in a religious minded world view (exploring this would be a separate post, it's simply a way of understanding the world I lack a better term for, I'd apply it to strict Marxists as well) that is coming into contact with our rather less religious society. For someone that believes that success and everything else good in life comes from God and proper religious observance there will be some severe cognitive dissonance. One way of resolving this is to think of the other society as a test. You saw the same thing in the West at various points in our history, the more successful society is there to test your faith so the answer to the challenge is to become more faithful and to fight back against the unfaithful society. The Crusades had some of this aspect, as did some other conflicts with a religious dimension, such as conflict between Latins and Byzantines.
What this means of course is that we have to learn to live with a low level of violence, it is not a problem with a solution. We already do this with domestic crimes, past societies have always done this with cross border violence as well. There is no way to restore the security that came with complete western dominance, that era is gone forever. Neither military effort or isolation and non-intervention will restore this past. The only way to end the violence would be to work to become less wealthy and successful than those discomfitted by our success, which would only spur our own religiously minded to get angry and fight back against this, or those other societies to attack. We need to learn to try to mitigate violence rather than try to solve it in a complete fashion.