JR was converted into 7 companies. Most of other 93 existing train companies were not paid for by government. Take Tokyo - The Keio lines, the Odakyu lines, the Tokyu lines, the Tobu lines, the Keikyu lines, the Seibu lines, etc... are all private and have been private since they started.
As for JR, most of the debt was paid back, at least by JR East and JR West.
https://www.google.com/search?q=is+the+london+tube+under+fun...
https://www.google.com/search?q=is+rome+subway+underfunded
https://www.google.com/search?q=is+barcelona+subway+underfun...
So you can claim, and I agree, that it's supposedly an investment. Unfortunately, putting it in the hands of politicians to fund often means funds are taken away for other things. Where as, the private Japanese train companies fund themselves and it works.
The trains in dense cities are well funded. Those in less dense areas have all the same problems as elsewhere in the world - JR Shikoku in particular is withering away. Having your quasi-public railway company engage in aggressive real estate speculation is great when it works (JR Kyushu) but the flipside is what happens when it doesn't (JR Hokkaido) - do you then hang them out to dry?
> And yet, no one will copy them. There's always some excuse. LA is going down the excuse route and adding train lines with no chance of ever supporting themsevles. They are all designed as a handout to the people who are too poor to buy a car, rather than viable alternative to cars, and the fact that they aren't connected to all of those extra things means they'll also never be as compelling to use.
All transport is handouts, only governments can really organise it and no single entity could ever capture all the benefits. The stuff Japan is doing right is mostly not subsidising cars (no publicly funded freeways, no handouts of public street space to people who are too poor to store their car themselves, no tax breaks for employer-provided car parking or company cars), and having sensible by-right zoning laws that make it legal and practical to build dense cities. But even then the various governments of Japan give a bunch of direct and indirect support to railway companies, and outside of the Tokaido corridor they wouldn't be viable without that.
And yet, no one will copy them. There's always some excuse. LA is going down the excuse route and adding train lines with no chance of ever supporting themsevles. They are all designed as a handout to the people who are too poor to buy a car, rather than viable alternative to cars, and the fact that they aren't connected to all of those extra things means they'll also never be as compelling to use.