Earlier quoted context omitted.
Tokyo
The only thing they have in common is that they're both near a fault line. Tokyo has a foundation of solid bedrock so soil liquefaction is not an issue. Very little of the area surrounding downtown Tokyo is sea, compared to San Francisco, which is a peninsula around 10 km wide.
http://images.slideplayer.com/22/6340453/slides/slide_27.jpg
If being surrounded by water is an insurmountable problem, how do you explain the tall buildings and subways in Manhattan?