I still think their attack was more symbolic than anything. I don't think they were as concerned in killing people as in making a scene. The WTC was the Mecca of free enterprise; the American way.
I'm also not so sure that they were in the know about the president's whereabouts, at least not when they were going through the process of buying tickets to these flights. I don't know when they had actually purchased the tickets but the info is out there. I'm sure the authorities know.
One last thing that I thought about: The concern over AF-1 as a target may have been symbolic as well. Perhaps they weren't all that concerned in hitting the actual plane. It may have been their way of saying that the President was the target. He is, symbolically, AF-1. He was wise to scramble. Also, I doubt if they could actually catch AF-1, particularly when he had fighter cover.
OK, one last thing; As I recall, in the WTC, it was the center core of steel columns that carried the brunt of the structural weight. Any hopes of cutting through the middle would have been pretty far-fetched. The plane would have sheered to pieces before doing very much damage to the supports. It was, as others stated, the heat that softened the steel and eventually brought the building down. Whether that was the plan or not is debatable. That it happened is tragic.