Specifically about the bullet trains, they are absurdly efficient in speed, they had to outpace air travel. Absurd speeds incredibly early on, and to this day only really China has surpassed them in terms of nation coverage and speed - a dominance Japan held onto for a good 50 years.
Fascinating to learn about, but not so great to apply blindly to other places.
The average person is willing to spend an extra 10000 yen to save 2-3 hours and the hassle of a flight.
Funnily enough, the business travelers I know in Japan actually take the plane, because it's cheaper for the company and they can keep the miles.
It's just the private version of transit-oriented development[1]. It's a good way to align incentives. The railway increases the value of the land around the stations, so the railway company gets to enjoy some of that benefit. Having the most salient product/service as a loss-leader for the real money-maker behind the scenes is a very common business strategy. Hell, it's how American railroads got built in the old West. It's how London became Greater London.
Many governments seem to have forgotten this basic stuff ... they'll do silly things like keep restrictive low-density anti-retail zoning codes in the areas around train stations. And then they wonder why the promised benefits of the railway didn't arrive and people still drive everywhere. Or they won't see any benefit to pre-emptively expanding the network into new places because "nobody lives there", reversing cause and effect.
[1] https://en.wikipedia.org/wiki/Transit-oriented_development