Tom, I too believe that the plane over Pennsylvania was shot down. When the plane abruptly changed course over Cleveland (it was already known by this time that it had been hijacked) two fighters were scrambled from the airforce base in Dayton, Ohio. They would've caught up with this plane precisely where the plane went down.
Also, there is reason to believe that the order had already been given. It's not clear if Bush had given the order, but it's fairly certain that Cheney had.
Moreover, Rumsfeld, in a press conference mentioned, "when the plane over Pennsylvania was shot down" then, after realizing what he just said, corrected himself. There's no reason to believe that the plane couldn't have been shot down, it has been a long standing policy to do such, just never been enforced before. If you recall a few years ago the situation with the golfer in a private plane that was flying around aimlessly over the midwest and ultimately crashed (they had lost pressure and everyone on board fell unconscious) the order had already been given to shoot it down, they were just waiting until it the debris would fall into a less populated area before shooting it down. However, the plane began to plummet before they had the opportunity they wanted to shoot it down. I think the administration just does not want to admit that they are responsible for the incident over Pennsylvania. Of course, it is entirely reasonable that they did not shoot it down, I just feel that, after three planes had been used as missles, they didn't want to take any chances and brought it down. By the way, it is possible to take a plane down without it breaking up into a million pieces.