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Isn't there a consideration of geological stability underneath San Francisco? I don't think much of the city could support tunneling underneath; large chunks are built on sand dunes and landfill.

http://priceonomics.com/what-parts-of-san-francisco-are-buil...

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The liquifaction susceptibility map shows that most of Market St is red. Seeing as that's where the existing BART tunnel is, I suspect it's not much of an issue.

I think the bigger issue is all the hills. They are bedrock, so arnt an issue for liquifaction, but make any underground line much more difficult to construct. For rail to get most places in san francisco its not enough to just rip up the street and put tracks underneath, like was done along market street. You need serious tunneling. Thats why historically transit in SF was mostly cable cars, which were replaced over time by buses. Its much easier to go over the hills.

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