I used to live in San Diego and was car-lite.
My first bit of advice is to get yourself a multi-gear bike (n+1 bike)
. San Diego has a mesa and canyon type terrain that can be pretty tough on a fixed gear bike. Hills like Texas Canyon just east of Hillcrest and Morley Field Dr. in Balboa Park between the Velodrome just east of Florida Canyon in Balboa Park and the rest of the park are good examples.
Actually you will likely want to visit the Velodrome in Balboa Park just to meet large numbers of bicyclists. It's close by Hillcrest.
http://www.sdvelodrome.com/
I would guess at your route would be down University to College to Broadway and follow it till it becomes Campo. I'm not sure you will want to use the public transit. You'll have to check. But for public transit you'll probably have to take the bus downtown and then make your connections either on the bus or trolley. The orange line on the trolley might make it a 3 mile ride to the trolley from your home, and then a short ride from the Lemon Grove depot to your work. Bikes can go on both the buses and the Trolley.
Yes, there are heavy traffic areas, downtown and on the freeways, but San Diego is pretty decent to get around in. It's fairly bike friendly. And the weather is very mild. There are neighborhoods in South East San Diego that you may want to avoid, but nothing worse than you might find in Philly.
Here's a transit link.
http://www.efgh.com/bike/transit.htm
There's lots of mountain bike riding opportunities in San Diego as well. (n+2, bike)