True but not the whole story, it is predominantly pvt but the model of pvtization is diff from what IR is following which seems closer to failed Brit model (some Brits themselves now looking to learn from Japan's successful pvtization)
https://twitter.com/JhaSanjay/status/1278922864389832709
Japanese rail can be
divided into: 1) private railway companies (e.g. Kintetsu, Odakyu, Seibu etc) which were always wholly private since their founding 100+ yrs ago 2) JR group, who r descendants of debt laden gov't run JNR which was slowly pvtized starting in 80's & split into JR East, JR Central,
JR West, JR Kyushu, JR Shikoku, JR Hokkaido, & JR Freight. Only 1st 3 were expected to be profitable though JR Kyushu has become so through diversification a couple of yrs ago. JR Shikoku & Hokkaido were not expected to be & as such gov't provided them stabilization funds when
they were born from JNR. They key difference between Brit pvtization of BR & JNR's pvtization is former runs on a franchise model & there is vertical separation meaning track is under ctrl of 1 company or gov't & trains r operated by a pvt company that won the franchise bidding
for 5 yrs, after 5 yrs bidding starts again. There is no vertical separation in JNR's pvtization meaning that JR East owns everything in its network permanently & can think & invest for long-term, see
https://twitter.com/Rjrasva/status/1157237905573777408
4) Third sector rail in rural areas, often single car
diesel trains run as partnership between pvt company & local gov't since they can't be profitable 5) Metro rail in big cities which r either gov't run or pvtized (Osaka, Tokyo subway is split between gov't Toei & pvt Tokyo metro).

So in summary: It's mostly private yes but not
wholly + the model of privatization for JNR was different from what UK had for BR with Brit model generally considered a failure by public with calls for renationalization.

Also people love trains just like hordes elsewhere love cars, there is a whole culture built around trains
& what they mean for Japan. So that means railway companies r not just out to make a quick buck
https://twitter.com/Rjrasva/status/1092394559533916160
I mean 30,000 rail fans flocked to a small city like Kudamatsu in Yamaguchi just to get a glimpse of a train Hitachi was exporting to Britain
30,000 rail fans bid farewell to Japanese train going to Britain

KUDAMATSU, Yamaguchi Prefecture--Tens of thousands of train enthusiasts and curious locals gathered for a rare glimpse of a new train bound for Britain
https://forum.lowyat.net/topic/4217068/all
This is an e.g. of a typical third sector rail called Tsugaru rail, run as a partnership between local gov't & pvt company
The importance & popularity of rail at a popular cultural level can be gauged by fact that Japanese celebrities do ad's for rail companies

This is Ishihara Satomi doing ad's for Tokyo metro. When was the last time Jennifer Anniston did an ad for NY Metro
Shinkai was asked why he seemed obsessed with trains in his anime, this was before he became a big name with Kimi no na wa (Your name) & he gave below answer:

http://www.electricsheepmagazine.co.uk/2008/06/01/interview-with-makoto-shinkai/
Rail privatisation: the UK looks for secrets of Japan’s success
Jan 28/2019
Robin Harding in Tokyo
The most basic, fundamental difference between the British and Japanese railways is how they were privatised.
https://ft.com/content/9f7f044e-1f16-11e9-b2f7-97e4dbd3580d
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