yes, there is sand and silt under parts of SF. new york is built on granite. the geologies are different. in sf you have to dig 15 stories for a basement. so its not just the seismic issues, but other factors of geology and geography: eg. you have the topo issues (hills). Then you have the SF summer/winds. Lastly, you have an existing stock of Victorian (actually, edwardian in most places) architecture that is worth keeping, for cultural reasons (/arguably).
Check out this interactive map of liquefaction risk. If you zoom into SF you can see that most of the skyscrapers are built in a high risk zone. Guess they figured it was ok.
Great link! But If you zoom in, you'll see the Marina, South of Market, and the edges in NB etc are "red" (the worst areas). This is exactly why the financial district (where the high-rises are) is located where it is (on Yellow to montgomery), and why SOMA was the "wrong side of the tracks". While they are/have been recently building high rises in the Red (embarcadero, etc), they have been digging 150 feet down (ie, 2x the normal height of an above-grouhnd building ~traditionally < 7 stories). to set the foundations. At least that's my understanding.
A ton of lower manhattan is built on fill so that doesn't seem to be a huge problem in building tall buildings. (Battery Park is totally fill, the Financial District is about half the size if you look at how big it was originally, so the rest is fill, etc)
The problem is fill in an earthquake, has risk of ~liquification. So its the combination of factors. NYC would have a major problem with a major tectonic event, for example. ~Nothing there is seismically zoned/engineered.