Let me say that I do not think the attacks could have been prevented. Even had the various intelligence agencies corellated all their data effectively, I do not think they had enough to put it together. Even hunting Osama Bin Laden intensively since then, he has not been found.
That said, I think that the real question here is, was the Bush administration nevertheless doing all that could have been done? Were they effectively asleep on duty? The answers here are clearly no, they weren't doing all they could have, and yes, they were negligent, and therefore they are at fault. If you are aleep at your post you are still guilty of dereliction of duty, even if the enemy attacks in another sector and there is nothing you could have done to prevent it or give the alarm. You are still at fault. Nero didn't start the fire that burned Rome, nor could he have prevented it, but it was still his choice to play the fiddle rather than do anything more constructive.