I often thought that even if they could have intercepted those planes, what would they do? Really shoot them down? With all those people in them? That would be a very tough call, because, what if they weren't going to crash into buildings? Then you would have to take the blame for killing everyone in the plane.
"But I thought they were going to ram the buildings! I'm sorry, I had to make a decision!"
"Trigger happy monster!" the people would cry.
And once they got over the city, shooting them down would have been even more dangerous. So yeah, good points.