Area 51 is frequently mystified in popular movies, stories, alien investigations, and sometimes, even the media. If the US really wanted to keep this a secret, why would they allow the media to mystify it so much. Is there any evidence to support that Area 51 is not a huge secret in itself, but, rather serves as a cover-up for secret operations taking place elsewhere?
The following answer is from "Expert Opinion" as a USAF Pilot, acquisition officer, and all around guy in the know. ;) I will endeavour to dig up actual links and such to support this. Bear with me before up or down voting.
Well, there is sort of a partial truth in that. Groom Lake has indeed been a classified location for a very long time. The US Air Force has developed, tested, and based aircraft such as the F-117 and even the U-2. These aircraft were designed to totally defeat anyone's air defenses, and in essence allow the USAF to violate sovereign airspace with impunity. Of course they didn't want anyone to know about this capability. (While it is Wikipedia, they actually have a pretty thorough article on Groom Lake.)
The reason the USAF doesn't talk about it at all is because no matter what they say, crackpots will believe what they will. Also, the less communication, the less of a chance that there will be an inadvertent release of sensitive information (after all, the F-117 was almost a total mystery until Operation JUST CAUSE).
On Nov. 10, 1988, the Air Force revealed the F-117 Nighthawk stealth fighter to the public for the first time.
The first F-117A was delivered in 1982,
Note the years. Having a remote base like Groom Lake allows for that (as well as other extraordinary security measures).
As for the physical location, it is well known, and before the government took control of "Freedom Ridge" people could even photograph parts of it. Also, you can request information from the DoD as long as it isn't classified. It exists, and again, for what the USAF is doing, the Wikipedia article is generally accurate.
That is not to say that there aren't projects going on there that no one really knows about. We may be developing some sort of micro-UAV, or a high flying persistent ISR platform, UCAV, or whatever. What one can say with confidence is that there are no "mystical" or extra-terrestrial artifacts there. The evidence against those items are supported by the whole of science.
And keep in mind, any government project is most likely not limited to just one location. There will be things that can only be tested at other places (like the McKinley Climatic Hangar). And some basic science may come from AFRL in Kirtland, Wright-Patt, or wherever. Any DoD program will by definition involve a much larger operation.