Since nearly the very beginning of Google proper (aka, not BackRub) they've had a separate search for government sites and for Linux. And also Universities... I vaguely remember both a University of Michigan and a Stanford search. (Larry Page was an undergrad at UMich).
it searches the .gov domain, because 'uncle sam' employees can't remember to put site:.gov in front of their searches ?
Think of it as a shortcut.
I'd guess over 90% of Google users (and maybe 99%) don't know about "site:" Hell, most people can't even come up with a reasonable definition for "search engine".