They are privately operated since the 80s, but the vast majority of their initial development was government funded.
As far as I understand the privatized companies are monopolies-- these companies were formed from the JNR by geographic area served (hence "JR East", "JR West" etc.)
In major cities like Tokyo and Osaka, J(N)R is far from the only player in town, there are numerous "really" private railways like Keikyu, Odakyu, Keio, Tokyu etc. And they all followed the same very profitable playbook of snapping up rural land, building a train line to it, and then building/selling off rights to build apartments, shopping malls etc on the now much more valuable land.
If you were to talk in terms of asset value, then yes, the government did fund most of it; but that was because the Shinkansen were enormously expensive compared to the old, narrow curvy mainline network. In fact, the large Shinkansen debts are why JNR had to be privatized; the government restructured the private groups so that all the debt was confined to a ‘bad bank’ paid for by the government.
That article didn't touch on what happened before JGR/JNR. Prior to railway nationalization around 1906-1910, most lines beyond Tokyo-Osaka were built and owned by private companies. This includes Sanyo Main Line (previously built and owned by Sanyo Railway, not to be confused with today Sanyo Electric Railway), and Tohoku Main Line (previously built and owned by Nippon Railway).
The original lines may be from the private era but JNR also built a lot.
The Saikyo, Keiyo, and Musashino Lines in Tokyo were all built by JNR. So was all the Shinkansen. And all the main lines around Tokyo were quadrupled or sextupled by JNR at great cost. And let’s not forget the feats of the Kanmon tunnel to Kyushu, the Seikan tunnel to Hokkaido, and the Great Seto Bridge to Shikoku.
Tokyo Metro and Toei are also state-owned, and private operators directly benefit from the through operations into the Yamanote loop.
As far as I understand the privatized companies are monopolies-- these companies were formed from the JNR by geographic area served (hence "JR East", "JR West" etc.)
The bloomberg story is really light on details for why and how the privatization occurred; for a much more in-depth view, see S.Y. Lee's Substack, for example this post: https://seungylee14.substack.com/p/the-death-and-privatizati...
(An interesting fact is that most of JNR's debt at the time was retained by the government while the assets and revenue were privatized)