To be honest most of the bay area is at best only slightly more affordable than San Francisco. According to trulia, median rent in Fremont is about $3200 (http://www.trulia.com/real_estate/Fremont-California/market-...), compared to $4500 in San Francisco (http://www.trulia.com/real_estate/San_Francisco-California/). Factor in the expense of a car, which is necessary in Fremont but not San Francisco, and the prices look significantly more balanced.

In this case, it seems like it would have been a better choice to build the school in San Francisco proper, than its outskirts. The marginal gains in affordability aren't worth sacrificing proximity to the tech industry.