From what I understand Tokyo and Japan in general have a lot of car owners (something like "one per house") or so, but they're rarely used for commuting purposes.
Exactly! If you only look at the commute, you get ridiculous things like commuter trains, that only run in the morning in one direction and in the afternoon in the other.
In the Netherlands for example, lots of people go by car to Work, because that’s relatively far away; but then they’ll use their bike or transport for everything else. Stuff like groceries, dentist visits, meeting friends, going to the gym, etc. because all those things are within (their district of) the city.