star trek - Why is Starfleet HQ in San Francisco?

San Francisco seems an odd choice for Starfleet Headquarters to me, especially within sight of the Golden Gate Bridge. It's such a densely populated area, I would figure that it's one of the last places one would want to place a new military facility - especially one which surely must be kept at the forefront of technological innovation.

If anywhere in the U.S., I'd more likely have expected Starfleet's home to be closer to an existing NASA facility that is more intimately involved in spaceflight operations. The obvious choices would have been Kennedy Space Center in Florida, or Johnson Space Center in Texas. The closest facility to San Francisco would be Ames Research Center in Mountain View, which doesn't quite compare to the other centers from the layman's perspective.

The next spot I could think of is Bozeman, Montana - site of Zephram Cochrane's flight of the Phoenix. But that's half-way across the continent.

Has there ever been an explanation in canon, production notes, or interviews, that explains why they chose San Francisco to be the home of Starfleet?

Answer

From San Francisco on memory Alpha, seems the reason was historical, both in-universe...:

Role in diplomacy

The city had a prestigious history as a place of peace. In 1945, the Charter for the United Nations was signed in San Francisco by some fifty of Earth's nation-states.
After World War III, the nations of the world met in San Francisco to negotiate a peace treaty. (ENT: "Demons")

The spotlight of diplomacy fell on San Francisco again in 2155, when the representatives of Earth, Vulcan, Tellar, Andoria, Denobula, Rigel V, and Coridan met in the city to hold talks on the formation of a Coalition of Planets. (ENT: "Demons", "Terra Prime")

Six years later, in 2161, the charter that lead to the founding of the United Federation of Planets was signed in San Francisco. (ENT: "Zero Hour", "These Are the Voyages...")

... and off-the-set:

Gene Roddenberry established the city's importance to the Star Trek franchise with the production and novelization of the first feature-length film, choosing San Francisco primarily because of its role in the creation of the United Nations. However, he also considered the city an appropriate showcase for the secular Humanism that underlined much of his own philosophy.