Where will you be storing the bike at work and at home? That's where your bike is spending most of its time and is most vulnerable to theft. Your bike is much more likely to be jacked when it's locked to a street sign overnight than it is while you're running into the grocery store or something.
Don't spend $1000 on a bike - spend more like $500. That's "doing it right." Get a
good lock - small u-lock with cable at a minimum - and
use it correctly. Get a seat lock as well (and don't invest in a super-nice seat), and don't use quick-release anything. Keep all your serial numbers and register them.
There is a really wide range between "beater" and $1000 bike. And "beaters" get stolen all the time, which doesn't necessarily cost you a lot of money (unless you just got it tuned up/got new tires/etc.) but does cost you time and effort.
Even in San Francisco, you don't have to have the most well-secured bike possible, you just have to have a bike that's better-secured than the other ones on your block.
What bike you get comes down to personal preference and comfort - for 20 minute rides you can ride almost anything (I alternate between a 55-pound steel behemoth with a basket and internal gears and a boring TrekFX 7.3 city hybrid).