We've sailed out of San Francisco a number of times. It is probably the worst port we've ever sailed into or out of. Traffic is a mess and if more than one ship is there at a time, it's even worse. If you arrive by bus from the airport, you may not notice but if you arrive by limo or other conveyance, it's a slow process.
We have cruised on Regal Princess round-trip out of San Francisco to Alaska. If you get beyond the transportation issue - sailing under the Golden Gate is one of the most exciting experiences of our seven cruises. I'd highly recommend it.
Yes, it's the worst port in the world in terms of getting there and getting embarked. It's crowded, it's disorganized, it's cold. But, it's also the best port in the world in every other way. It's a magnificent experience to sail out under the Golden Gate Bridge. It's also a wonderful pre/post cruise city!