1. Even if an order had been given to shoot down the plane, it would have taken far too long for even an F-15 or F-16 to arrive on the scene. As we learned on 9/11, it's not as if there are a bunch of these aircraft sitting on tarmacs with pilots in them just waiting for an order to take off.
2. The U.S. Navy was apparently conducting some kind of exercise off the coast of New Jersey that evening, which put them in a fairly good position to respond to an emergency of this kind.
3. There are a variety of different eyewitness accounts regarding the "missiles," but from what I understand, all of them can be clearly assigned to one of two different missile trajectories. This is what led to some speculation that the incident was actually the result of a military test gone awry (i.e., the Navy was testing a missile by firing at another missile or a drone of some kind, and the interceptor took down Flight 800 by mistake).
4. While covering up such an incident would be difficult, it certainly would not be impossible. I understand that the crews of the Navy recovery teams at the site were subject to some kind of unusual executive order, and there is clear evidence to suggest that the U.S. military has attempted to cover incidents up before (remember that explosion in the gun turret of the U.S.S. Iowa, in which the Navy tried to pin the blame on a "gay" sailor?)
I thought the article attempted to show that a lot of people in different places saw the same object, but in different trajectories, based on their positions.
Unless a military training accident was orchestrated by incorrect information to ensure the elimination of one or more passengers (possible, but not probable), deniabiliy would take precedence over truth (even in the Clinton era), as there were loads of French nationals and children on board.
Most likely, a terrorist act. Testimony from numerous credible witnesses of apparent missile sightings was ignored. Not denied, just ignored, much as testimony regarding ME looking individuals in the company of Tim McVeigh on the AM of the OK City bombing.
It is likely that Flight 800 and the Murrah Building were both terrorist acts with ME participants, but the former was denied to keep the Clinton economy looking good, the later to use as a political shield against the conservative right who were pushing hard for an investigation into federal actions at Waco.
Finally, 9/11, an undeniable event, opens America's eyes....