Yes, many of the transit companies in Japan are really more accurately described as real estate companies that own and operate train lines. Most of their profits come from the real estate, not the trains, and the trains are mainly a way to get people to go to the properties.
One big difference you can see between the US and Japan along these lines is the stations: in the US (and Canada from what I've seen), there's absolutely nothing inside the stations, just fare gates and a platform and train tracks. In Japan, the station has vending machines, shops, underground connections to nearby buildings, spaces for vendors to set up temporary stalls, etc. In the high-traffic stations, it's easy to stop in a convenience store, or in a Starbucks, before getting on your next train, and of course the train company is getting money from that in the form of rent. Some really big stations have larger shopping areas attached. But the US seems allergic to renting out commercial space in stations for some reason, and wants transit systems to get all their funding from fares and taxes.