Parking just adds $200-$300. (I could be wrong but I feel that it's also tax deductible if you keep the receipts.) It's still a lot cheaper by approximately $1000 depending on your living situation (It's even cheaper if you just rent / sublet a room outside of SF: $600-$900 including utilities). I used to do the same thing even though I could have taken Bart instead which would make it a lot more affordable and healthier from all the walking.

As for time my drive was about 15-20 min one way and I used it to listen to podcasts and audiobooks. For Bart, I would either work, sleep, or listen to podcasts plus I saved a lot of time and money that I would have used for a gym.