The train companies in Japan, while private in name, can only be described as hybrid. They have massive gvmt concessions for land to build their malls and make profit. The gvmt also has a lot of direct and indirect influence on them (and the other way around). In fact I'm literally now in one cafe in one of those malls, I haven't used the train today but still a part of my money goes to the train company thanks to these concessions.
I'm not complaining BTW, love the train system here, it's only when someone tries to describe them as either a purely "private" or "public" company it's never so straightforward IMHO, so wanted to clarify.
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.