Why alien conspiracy theories just don't hold water
It's not that I don't think it's entirely possible - or even quite probable - that the government and/or military has kept us in the dark and fed us misinformation about a number of things that have happened throughout history.
Regarding alien conspiracy theories, though - that the government and military have known for quite some time that extraterrestrials are among us, and that close encounters are routinely covered up and suppressed - it just doesn't seem possible. Again, not because it's inconceivable the government would intentionally mislead the public - but for the simple fact that if alien encounters were really commonplace enough for the government to be involved, at least a few non-blurry photographs and semi-coherent accounts would have slipped through the cracks and made their way to the general public.
If you take this movie as an example - it was only sheer chance that the only two survivors ran straight into a military team that 'took care of business.' If, as alien conspiracy theorists assert, alien encounters are commonplace, at least a few people would have managed to evade the cleanup crews and made it back to civilization to share their story - along with a few photographs, given that nearly everyone has a camera phone these days. And even if the government could track down these witnesses and silence them, surely at least a few photos and videos would have made their way to the internet where they would have gone viral.
Makes for an entertaining movie or TV show. In real life, though, it's probably better to worry about pedophiles and drunk drivers.