See the earlier comment, the large Japanese private railways are real estate and hospitality companies with a train side business. Each has built their own little fiefdom, but they play nice enough (thru trains, tourist passes, and regional transit payment cars) to make all the effort not worthwhile.

Although during WWII and for some years after all the lines to the south and southwest of Tokyo were under Tokyu Railways (then known as Dai Tokyu, or "Big Tokyu).