I live in the Bay Area as well. All I can say from previous entry level experience is to try and purchase used if your ego allows you. Why? More than likely you will get a $2k bicycle and components for the $1k budget you have. Craigslist is your holy grail.

If you are just using this for commute and occasional weekend ride, even all the more reason to buy used. There are some seriously good used bikes out there.

The main difference in price points are the components and the frame material. Do some basic research and then tell us what kind of frame material you prefer (Steel, Alum, CF). What about those Cannondale's attract you? Another reason why I recommend used is so you can have a good idea after 6 months of cycling what it is / isn't you like about your bike that you'd like to change. Allows you some wiggle room to help define what kind of bike you are seeking by actually owning one. It's comparable to "What should my first car be?".

After my first road bike purchase, personally I feel the better the component quality is, the more you can surpass the quality of the frame (I'd rather have high-end campy or SRAM components with a heavier frame).