||The facts surrounding the downing of the fourth plane are undoubtedly odd. It's true that a case can easily be made that they indicate its having been shot down, while it is very hard to fit all the facts listed here into any theory that doesn't involve a military interception. The unusually localized crash site, the reports of explosions and smoke while the plan was still airborne, the apparent lack of significant debris. The failure of any information to emerge on exactly how the crash came about is concerning, and the absence of any visible serious investigative reporting into the peculiarities of the case also serves only to increase suspicion, although this at least can be reasonably explained by the lack of competent investigative reporting into anything these days.
However, while the 'official' explanation seems hard to justify in the face of contradictory reports, it is not impossible that it is correct. The most damning pieces of evidence tend to be single-observer accounts arising in the immediate aftermath of an extraordinary event. They are small observations, never independently verified. Past and very recent history shows us that even when carried by major news networks, reports of this kind can still turn out to be fallible. The crash site does look very different from other sites, but as has been pointed out, we are not aviation crash experts, and we do not know what a terrorist-piloted flying bomb impact should look like. Deliberately crashing the plane in order to kill the passengers in lieu of a major target is a credible explanation, and if we want to compare the resulting impact site to similar events, we don't have a lot to go on.
So if we look only at the direct and reported evidence concerning the crash, it does tend to support the theory that it was intercepted, while still allowing a--narrow--possibility that it was not. But what happens when we examine the alternative thesis?
I think we have to assume that if the plane was shot down, then subsequent action was taken to hide that fact. The standard of investigative reporting today is bad, but it's not so bad that a domestic missile strike on a large airliner could go unreported without some degree of coverup. So if a coverup happened, there are two questions to consider: why and how.
Let's start with the 'why'--the will to deceive: if the suggestion is that the government is trying to cover up the destruction of the airliner by the American military, then please explain to me: why? They are perfectly happy to tell the public that they planned to do so; according to them, the only reason they didn't is that they didn't get there soon enough. Open kimono time: yes, we tried to shoot it down. We failed, but we did try. How could reporting that they were successful actually be worse than that? Further, imagine the propaganda benefits of a successful interception. "Not only did these evil people attack our citizens, but they forced us into the horrific situation where we had no choice but to shoot down our own civilian aircraft in order to save a larger number of lives." Oh, the humanity! Surely this is a military propagandist's dream come true.
Let's put that aside, and assume for the sake of argument that they do have a valid reason to cover up a successful shootdown. You have a large plane shot out of the sky, inevitably resulting in widespread debris. You have to start by preventing access to that debris in case somebody finds evidence of military hardware or its effects. You have to keep from the media every possible transmission from the plane (or nearby) that suggested a military intercept. Then you have to silence everybody who might have received such a transmission. And everybody who might have witnessed the intercept from the ground. And everybody that any of these people might have spoken to before you identified and got to them. And every member of the military involved in the operation. And, before anyone that you miss has a chance to slip a story to them, you have to immediately silence all the media, those lovely people who balk even at editing broadcasts from the Evil One himself in case they contain coded instructions. Plus you have to convince them not to report that curious people are (presumably) being kept away from the crash site. And you have to start doing all these things immediately, you have to keep it up for the forseeable future, if not for ever, and you have to get it right every single time and not let a single piece of information slip out of your net.
Could this actually happen? Technically, yes. Practically, what is the likelihood that American military and intelligence agencies could achieve that level of effectiveness from a standing start? How does that probability stack up against the possibility that the reason why the impact and other associated reports seem to indicate a military shootdown is simply that we are dealing with an extraordinary event, the nature of which means that it is never going to yield up a useful quantity of simple, obvious facts.