To not consider planes being used as missiles is just nutty, in my view. A terrorist can use a truck as a bomb, but not a plane? Come on.
But anticipating a general event and stopping a specific one are two entirely different things. Hindsight is just wonderful, ain't it?
There was an attempt to hijack a plane and crash it into the White House in the 1970's. The CIA had evidence of two other plots - one to crash a plane into the CIA HQ, and one into the Eiffel Tower. Clancy wrote about using a plane to crash into the Congress.
I'm very uncomfortable when our NSA says that she couldn't have imagined anyone hijacking a plane to use it as a weapon.