Ooohh, I did this a couple of years ago when I was in the Bay area for a cousin's wedding. I arrived a day ahead of most of my family, so I rented from these guys: http://www.blazingsaddles.com/

I rented the "comfort hybrid" and they provided helmet, lock, rear rack, and handlebar bag. You can take a look at the maps they have on their page. Most people only do the "Bike the Bridge" ride, but I went a bit further on their "Presido and Golden Gate Park" route. It was fun biking close to Ocean Beach, and yes, the hills are tough. I ended up walking up one of them since I wasn't used to hills being so long. I got lost in Golden Gate Park (The City needs to mark their streets better!) and had lunch in the Haight, then back up to the Presido where I got lost again. Then I went over the Golden Gate (watch out for pedestrians on the bridge, especially when it's nice out) and down to Sausalito. When I got down to the docks, I found out my family was still in rental car hell, so I went on to Tiburon. Took the ferry back.

Even with the getting lost, I had a blast. It was neat going down residential streets to just to look at all the houses. San Francisco is a great city. I cut it close time-wise when I was catching the flight back, because I didn't want to leave.

I would change one thing if I did it over again and put in the same mileage as last time: I would pay the extra money and get the road bike instead of the hybrid. I was essentially on the bike for most of the day, and since the hybrid had a more upright riding position than I was used to, my butt hurt. And that was with wearing bike shorts. But if you're not planning on riding quite as much, the hybrid will be fine.

Hope that helps, and have fun!