I realize I'm the lone voice on this, so I'm going to say it again. Stay in the city!!
You can easily catch a cab out to the airport in the morning in about the same amount of time as an airport hotel shuttle. "You never know what can happen." Well, the airport shuttle could break down too.
Stay in town, have a nice dinner, perhaps a last cable car ride over to the waterfront, a last Irish Coffee at the Buena Vista, a last view of the Golden Gate Bridge. Then tuck in and get up early in the morning.
At 5:30-6:00AM it's a very quick trip to SFO. I should know, I spent 10 years making the commute to the airport.
Why waste a night at a nameless/faceless airport hotel?
And who cares even if you do have to get up a bit earlier? You can sleep on the plane.