I watched a rather interesting YouTube vid about no-fly zones last week. Area 51's airspace is one of the most restricted in the world, even more so than the area over the White House. Most important sites have a restriction up to a few thousand feet, but Area 51's restriction is from the Earth's surface to unlimited altitude for all aircraft.
The same video also said that Walt Disney World and Disneyland both have permanent no-fly zones over them, since 9/11
I think its just very, very hi-tech military/espionage stuff going on there, not the Roswell kind of thing.