You will see all sorts of bikes commuting in SF, from hipster fixies to $10k carbon road bikes.

I would think about a few things

1. would you want a rack or would you use a backpack? If yes, then you need a bike that can handle a rack0
2. Will you do this ride when its raining or wet from fog? If so you might want a bike that can take fenders
3. Will you use this bike for anything else? Longer rides around SF? A weekend ride to Sausalito? That may influence what you want.

Ultimately, you want a bike that is comfortable for YOU. This is a short commute with limited hills, so anything with some gears will probably manage just fine.

I suggest going around and trying multiple bikes at multiple bike shops. Find what is comfortable for you. If you are having trouble deciding between bikes at different shops, pick the shop you think will give you the best service.

Finally, do you care about style or just practicality? Some people want to make a fashion statement with their bike in SF.

There are a ton of bike shops in SF, many of which are walkable from Cal Train: Mikes bikes, Pacific bicycle, Marin factory store, etc.

I would probably suggest a hybrid or "flat bar road bike" type bike for this. I know Marin has some nice bikes (Lombard, fairfax, etc) and you can often get a last year model cheap. Specialized Sirrus would be good for this too (Mikes bikes).