I am in SF also. My commute bike is a Marin Muirwoods 29er, but the top tube is sloping and it is more like a mountain bike than a road bike and the tires are 42mm. I find that the bigger tires are much more comfortable than the bike I tried with 32mm tires. It is a bit on the heavy side though, about 30lbs or 13.5kg so you might find that unappealing. The Marin store on 7th and Folsom has a 25% discount on their previous year bikes so that might be worth a look.

Other bikes you might consider are one of the Jamis Coda or Jamis Satellite bikes. Both are steel bikes but teh top tube is not horizontal. The Kona ***** Tonk is a steel bike too.

The Jamis Commuter bikes might be woth a look too. They are steel with slightly swept back bars and they already include fenders and rack.