I totally agree it's possible to be prepared, but if you're talking about the earthquake I'm thinking about from May - http://earthquake.usgs.gov/earthquakes/shakemap/global/shake... - I don't think it's a great example, since the epicenter was pretty far from central Tokyo and also quite deep (153km) so at the surface it wasn't particularly strong.
Apart from being centered very close to Napa this earthquake was also fairly shallow (10km) so it was significantly more intense (albeit in a small, not heavily populated area) even though it was of the same magnitude. http://earthquake.usgs.gov/earthquakes/shakemap/nc/shake/722...
(I say that based on the numbers, not having first-hand experience with either quake)
I'm not arguing that you can't prepare for this - but a 6.0+ is just going to do a lot of damage, regardless of how much you prepare. Roads will be torn apart, older buildings will shatter, fires will be started, etc...
Preliminary reports put the damage to in California in the neighborhood of $1 Billion.
It's important to repeat that this was the biggest earthquake the Bay Area (an area that certainly gets its share of earthquakes) has seen in 25 years.
Granted a lot of infrastructure is equipped for this (gas was shut off in my apartment for example), but it's possible to be prepared for this.