The government is hiding something everywhere. Area 51 however, probably but also probably not what you'll expect. If they have some facility that deals with evidence of an extra-terrestrial nature then I'd imagine it would be such a secret location that it'll never get mentioned by any media outlet or movie.
So what could they be hiding at the infamous Area-51? I would guess its reputation. Its probably home to something boring and nowhere near as impressive as a shot ufo.