Wreckage was not spread out over several miles.
There is no evidence the plane was shot down. None.
In addition, that would be the secret too big to keep.
Not only that, we KNOW there is no secret. The government has openly admitted all along that the order had been given to shoot the plane down. The fighter jets just didn't get there until a few minutes after the plane went down itself.
Of course, there are a few who manage to spin a conspiracy theory out of this anyway, alleging that there's some wacko reason why the government will admit to giving the order yet not admit to "actually having it carried out." They just never get around to giving an explanation for such an argument that makes even the slightest sense. (Usually it's the standard hoary line that only worked up until 9/10: "The public wouldn't be able to handle the truth.")
In the end, interestingly enough, it's rather like the hair-splitting article that launched this thread. All that matters is that the government intended to take that plane down and has let the public know it. Once that's been established, what's the difference whether it went down due to an Air Force missile, a revolt by the passengers, or the actions of the hijackers themselves?