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
And that is why rail is so expensive in the States; transit decisions are not made on the basis of profitability.
(Note that in the case of Japan, some of these private rails were converted to "Third Sector" aka public-private rails, where they continue to be run by the private rail company under the financial subsidy of the local prefectures through which the rail line runs.)
I'm sure there are some differences, but this is true for Amtrak in the US too
The Japanese countryside is ageing and depopulating. Any railway operator, public or private, has to face this reality. You can either shut them down, or reduce service, or subsidize them; all three are painful in their own ways, and all three are done in different places, depending on local conditions.
Furthermore, a line may be "unprofitable" on paper, but still be worthwhile overall because of network effects.
The rural decline is at least being managed with more rationality than the senseless Beeching cuts[1] (and at that time, British Rail was wholly under state control).
It’s sometimes insane how lines are kept running in Japan.
Tokyo Metro: 100% owned by the Government of Japan and the Tokyo Metropolitan Government.
Toei Subway: 100% owned by the Tokyo Metropolitan Government.
JR East: The vast majority of their infra was built before privitisation using cheap or free gov't money. Also, during their 100+ year build-out, the Japanese gov't would regularly favour their own national system over private systems (grants, loans, approvals, etc.). This gives them a huge economic advantage that lasts today.
Better than British railways (and energy suppliers). Private companies with a government as the biggest shareholder. Just not the British government ...