Suppose TWA flight 800 was hijacked. The terrorists would not have made their move until the plane had gotten near cruising altitude (to avoid an accidental crash). Between that point and the time of the supposed shoot-down, there would have to have been a radio transmission to let the government know what was happening, then the word would have to have been passed up the chain of command to someone able to make that decision, then orders would have to have been sent back down the chain of command, then a plane or ship would have to have been sent to intercept the airliner.
I don't think there was enough time for all that to happen. If the Navy and/or Air Force had standing orders to down all hijacked planes, they wouldn't have been able to keep them secret.
Besides, did the plane make any course changes that would have suggested it was heading back to land to crash into something?