Japan knows a thing or two.
Japan is one of the most earthquake- and tsunami-aware countries in the world. Considering its geography, the bad luck of such an unprecedented incident (an 8.9 hasn't been felt in Japan in recent history, so no serious information to work with) has been tempered significantly with planning. It's just that, in this case, even the best-laid plans go awry, especially when you get big tsunamis right after the quake: not giving people a lot of time to head for high ground.
To answer your question, people have been researching seismic isolation and other earthquake-mitigation strategies for decades. Japan and California keep trying out new ways to keep the shakes from toppling buildings and the like, and considering the magnitude of the quake, it seems it's been helping. Japan knows it has to live with earthquakes, so it plans for them (think of this: the Akashi-Kaikyo Bridge crosses a seismic fault line). Odds are the nuclear plants were built with seismic isolation. It wasn't so much the quake that's putting the plants on the brink but the flooding from the tsunami (blame that on lack of data: Japan hasn't had to deal with a tsunami this big in recent memory; California has that problem every so often as well).