The scale of the September 11 attacks was greater than most predictions (given that no terrorist attack in history had ever been that destructive) but planes into buildings and terrorist attacks on the WTC were frequently predicted events.

The Empire State building has been hit multiple times by planes including a serious incident involving a B-25 in 1945:

http://en.wikipedia.org/wiki/B-25_Empire_State_Building_cras...

and the WTC had been the subject of multiple previous bombings:

http://en.wikipedia.org/wiki/1993_World_Trade_Center_bombing

Planes attacking buildings – especially the World Trade Center – is certainly something that had been imagined.