Yeah, the big JR (Japanese Railways) companies that were created when the JNR (Japanese National Railways) state owned company was privatized really do seem to operate in some form of hybrid way - not really either private or public/state owned.

But its also important to note there are other still big but much more private players like Kintetsu, Hankyu, Keio or Tobu that also follow the same playbook - having not just rail lines but also malls, hotels and other businesses, like: * cableways (like the Kintetsu Beppu Ropeway) * zoos (Tobu Zoo) * theaters (Takarazuka Revue - all-female musical theatre troupe based in Takarazuka - a division of the Hankyu Railway company - all members of the troupe are employed by Hankyu)

And you can see this replicated on the smallest level - when we went to Izumo, we found out the Ichibata company does not just run the line to the Izumu shrine, but also owns a hotel next to the Izumo station, runs local buses and even runs the gift shop in the Izumo museum. :)

I think this can to a degree explain why public transport is so well connected with other services in Japan & why the stations are clean and convenient - it has a direct benefit for all the many side businesses the public transit companies have.