In my opinion, I believe you'd have the same scenario as 9/11.
I don't believe the hijackers would hijack the plane too early in the flight, therefore helping their cause of "surprise" attacks.. If they hijack the plane 20/30 minutes out of New York/the US, there going to be shot down or escorted to the ground via fighter jets OR
subdued by the pax/crew. NO one is going to let a terrorist take over a plane again, trust me. Since we all now know that it's a hopeless cause (i.e, if there's a bomb on board, you have a 50/50 chance of living or dying, so you might as well try to turn the tide of luck on your side).
If this were to ever happen again, I don't believe we are adequetly protected, even though we are being assured we are. Look at the stupid Canuck (Canadian) at the Olympics. 1.x billion dollars of security, and some guy in a tutu just walks into the swimming pool and dives off the diving board. Perfect example.
The only way they would be able to do ANYTHING about this, was if someone on the plane was able to communicate to the ground that they were being hijacked. In which case, the US would take appropriate action in removing the danger to their Homeland. If this meant taking the plane down with a missle, then it's going to go down.
This 'shooting down' of aircraft has occurred in other countries before. I believe China and Russia have both shot down Airliners whom were supposedly in restricted areas. No negotiation, just shot down. The US actively tries to dissuade terrorists from doing what they are going to do, and if that doesn't work, they need to resort to the same manner. 200-300 people dying for the sake of 3,000 isn't any easier to swallow, however it's the honorable thing to do.
This is the scary part of terrorism. The terrorism isn't the hijacking. The terrorism is the "what ifs...." that come with the threats.
Lets hope and pray to whomever you choose to pray to, that this won't occur ever again.