from MeFi: a report of passengers on the PA-crashed flight attacking their captors. then the discussion included this quote:

One other thing I heard last night is that pilots are trained to comply with terrorists. In almost all aircraft hijackings, no innocent people end up dying. In those that due, it is usually due to botched rescue attempts, not terrorist action.

Naturally, none of the pilots which commanded the planes that flew into the WTC and the Pentagon could have ever reasonably assumed what was to happen to them. They would have cooperated with the hijackers until it became obvious what their plans were.

To which I posted the following response:

also, since the reported evidence and resulting speculation points to trained pilots among the hijackers, the legitimate pilots were probably replaced and held with the rest of the passengers, having even less abilit to intervene if intentions became clear.

maybe the hostages of the PA crashed flight overwhelmed their captors. maybe the captors had told them their intentions by then, maybe bragging about preliminary reports. mabye the hostages had even heard what was happening via cell phone and put two and two together. maybe they took out the captors in the passenger compartment, stormed the cabin, and the captor pilot crashed the plane.

these are wild speculations, but it seems a plausible scenario, at any rate.