I live and work in Novato, so I pretty much try to avoid the traffic. If I go to the city outside of the heavy traffic hours, I can pretty much be in Outer Sunset (where my sister lives) within 30 minutes, and in downtown, Market street within 40 miuntes if not less.
However, my husband commutes to the city every day and he does have to negotiate the heavy traffic.
There are several ways to commute to S.F.; by car, by bus or by car then ferry, which is what my husband does mostly.
If you drive, you would take 101 South. The traffic backs up a bit where highway 37 merges in from Vallejo, going towards Freitas Parkway in San Rafael, and finally where the three lanes 101 merges into 2 lanes around Lincoln in San Rafael. Heaviest traffic is between 8-9, but otherwise, it's much better. That's why I think South Novato around Hamilton, Ignacio, Country Club, Indian Valley and Pacheco Valley are popular with commuters
There are some local routes you can take to avoid heavy traffic at places. If you call me or email me, I will be able to help.
You can also take bus into town. There are quite a few bus stops and the schedule is pretty user friendly for commuters. UCSF has a bus going to various UCSF campus. My son took that when he did internship there. However, you do have to be careful of when the bus stop running. If you missed the bus, you might have to take the ferry.
My husband loves the ferry. That's when he can relax, rest and enjoy the ride - what better way to commute to the city than being on the gorgeous water and enjoy the wonderful, million dollar view! The riders on the ferry are very considerate and it's usually very quite in the morning.
Feel free to call me or email me with any questions. I would also love to help you find a home in Novato or other Marin county cities to fit your needs, whether it's commute, family, school, entertainment, ...etc.