There was never much doubt that Area 51 was a testing ground for experimental aircraft. And with the global climate being as it is, not much reason keeping it a "secret".
As for the alien conspiracies, the military must have thought they struck gold as it provided a perfect cover as people chased UFO's and would never believe the truth even if it was staring them in the face (as it is now). Makes it even easier to cover up the real reason for being out there in the desert and keeping the real technology a secret form the U.S.'s enemies.
Besides, everyone knows aliens hang out in crop fields and not deserts