Japan makes car ownership ridiculously expensive and inconvenient. People spend an average of 100,000 yen on a car per month, that’s a third of the average monthly income.
Speed limits are low across the board, and there’s tons of traffic calming such that a trip by car is often slower than by train or bike.
Yes, Tokyo has the best public transport in the world, but people would still choose cars if they were faster and cheaper.