Hey there Umeboshi.
Well, obviously if you want to live within a walking distance from school, then your husband would really be doing all the commuting, right ? Poor guy ...

It is possible, though, but I would strongly suggest that he invest in a car (which when you come to think of the cost of the commute on the long run, is not such a bad idea).
Anyways ... most of us live in San Francisco proper (the city itself, not south San Francisco or the bay area). It is just more convenient. School is very demanding, and there are times where you will just need to run home for a quick meal and head back to school for lab work or whatever. It pays to live close to the school.
Having said all that, we do have a couple (maybe 3 or 4 actually) of us who commute every day. All married and some have kids. If they can do it, so can you. I am sure they would be willing to give you plenty of good advice once you get to know them.
One of them lives as far as San Mateo. That is about half way between SF and SJ. Further more, it is more family oriented (than SF city), and offers a wider variety of housing options, specially if you have pets. Needless to say that it is more affordable than the city, which is a big plus (rent will make up for a big chunk of your monthly expenses).
The main transportation throughout the bay area in general are MUNI (the bus) and BART (the subway).
The BART goes as far south as Millbrae, which is a bit south of the SF airport. All you need to do is take the MUNI from school to downtown, then hop on the BART. Pretty straight forward.
Another thing you may want to consider is how late all these things run. You may need to stay late at school for one reason or the other.
In the end and in all honesty, I am not the best person to ask about this since I do not have to worry about family/kids/pets, and I live 3 minutes away from school.
I just wanted to share with you some of my thoughts based on what I've seen other people go through, and my brief knowledge of some of the city's insights.
Here are the web links you need in order to do more research on your own.
http://transit.511.org/tripplanner/index.asp (trip planner)
http://www.bart.gov/stations/map/systemMap.asp
www.SFMUNI.com
www.maps.google.com
http://sfbay.craigslist.org/apa/
I hope this post helps you in any way.
Happy New Year and Good Luck.
Hi NileBDS,
Thank you for your response. You have been very helpful to everybody here in this forum. My husband works in San Jose. Correct me if I am wrong but is there any other mass transit system besides caltrain that goes to San Jose from San Francisco? I would like to live walking distance to school but I guess we have to compromise so that he can take the train down to work. Where do most of Pacific students live? Thanks again👍