I tend to agree, BUT if these are so common, why didn’t our government say immediately it was a plane, even give the flight number. Why so hush hush and why still so vague on the matter?
Really, that's the clearest indication it's NOT a coverup. If they came out instantly and said 'oh, yeah, that's a UPS flight or flight 808 out of Hawaii inbound for Phoenix', I'd probably be on the side of the missile theory. Of course they'd have no idea what it was that was filmed, all they'd know is a) They didn't launch anything, b) the FAA didn't report any missiles, and c) their own detection systems didn't report any missile launches.
That someone went digging long and hard to find another angle of the 'missile', lined up the shots, used Google Earth to match up flight paths - I know a lot of us would like to imagine our government doing that, but I've yet to meet a public employee who'd show that much imitative.