It was Sunni Arabs from those countries in the Middle East which had the closest ties to the U.S. including Saudi Arabia and Egypt. If there was ever an indictment of a Wilsonian foreign policy, it was what happened on 9-11. Um, wait a minute... How is that an indictment of "a [supposed] Wilsonian foreign policy"?
You yourself point out our attackers were from Saudi Arabia and Egypt. But those are exactly the places were we did NOT follow the advice of the e-vile and dastardly "neocons," and determinedly promote democracy; but instead followed the dictates of the contrasting foreign policy "realism" which you advocate, and tolerated or supported authoritarian regimes.
Egypt and Saudi Arabia did not have democracy but comparatively speaking their young people (especially the hijackers) had more much exposure to Western democratic and market institutions than other parts of the Arab world. I agree, however, that this wasn't the main factor. They didn't hate primarily because we are free but because we are "over there" in a more direct sense. It is no coicidence that hijackers came from those countries which had U.S. presence (including troops).
I do not advocate the amoral version of realism you lay out. I advocate a policy of national defense and non-interventionism.