Well, gotta disagree a bit here.
Its been known for a long time that Osamas lot wanted to spill American blood, remember the World Trade Centre. So we knew they wanted to go for big buildings.
Other terrorists have attacked public transport (Israel, Japan etc), and terrorist plane hijackings have been quite common. So we knew they weren't afraid of hijacking planes.
This type of strategy had been used before (Lockerbie), where numerous deaths ocurred on the ground. So we knew they had seen the potential of using a plane as a bomb.
Furthermore Osama has a university degree in Engineering, thus maybe attracted to larger structures as targets.
The plans had already been found by police on a laptop in the Phillipines 6 years earlier, the Israeli Mossat warned the FBI about the attack, a flight instructor warned the FBI about Moussaoui. And there was loads of other anecdotal evidence (such as the flurry of activity among terrorist groups for 6 months prior to the attacks with pretty much all secret service organisations aware something big was coming up, and it involved airplanes).
I think the failure was in putting all the evidence together. I suspect they may eventually discover the FBI or CIA knew about this but just didn't believe it. The cover of "interests of national security" also allows the secret agencies to conceal their mistakes, will the truth ever be known?
Lazza.