I have made the trip from north Marin to Presidio countless times at rush hour. Mornings flow very well and it only takes about 25 minutes from San Rafael, once you are on HWY #101. Coming home, as mentioned below, is another story. Count on 30 minutes if you leave SF by 4:00. After that, it starts to back up and can take up to an hour in extremely heavy traffic. Thursday afternoons seem to be exceptionally heavy, with the Friday of a long weekend being the worst.
Hope that helps.