I recall watching Star Trek : The Voyage Home and thinking it was cool detail that it was set in San Francisco. That of all places in the Galaxy and Universe, Star Fleet Headquarters is based in the City by the Bay.
What really made San Francisco special, Bernardi says, was its progressivism and diversity. Roddenberry was a liberal humanist, and San Francisco, out of all American cities in the 1960s, best captured the issues Roddenberry wanted to delve into in the show. It was a hub for the civil rights and anti-war movements, says Bernardi, who has studied Roddenberry’s papers, which are collected at UCLA.
SFGate.com, Victoria Sepulveda, ‘Why ‘Star Trek’ made San Francisco the center of the universe’