I live in Tokyo. The rail network here is so dense that even locals like me still get confused figuring out transfers sometimes.

One thing I don't see discussed enough: the cost of car ownership in Tokyo is a huge factor. Monthly parking alone can cost as much as renting a studio apartment. In central Tokyo, parking for a single day can run close to $200.

When your country is this small and land is this expensive, trains just make more sense for most people. I think the rail network developed as much out of necessity as anything else.