Tony Stark has the resources to buy whatever he wants, whether that happens to be advanced technology, or that bar General Ross is drinking in at the end of The Incredible Hulk.
In the comic books, that also includes Area 51, the US government's shadowy research base. Stark acquired the site in Avengers #19, but why he purchased it has never been revealed.
Presumably it's the ideal place for him to work on new Iron Man tech away from prying eyes, or maybe he wanted to pillage the alien artefacts that are rumoured to be housed there for his next suit of armour.
It did come in handy down line when Stark was charged with hiding the Reality Gem, but his ownership of the facility has never been referenced since that.