When the towers were first built, one of the design questions was whether or not they could survive being hit by a 747 — on accident, presumably. So, that issue was taken into consideration.

At the time of the attack, more modern aircraft were used, which had much thinner skins and were much more lightly constructed. Which means that they got much more shredded by the building construction as they passed through, and which also helped take off a lot more of the fire insulation from the trusses in the building.