Every major station I went to in Japan had a huge mall with restaurants connected to it owned by the rail company. Inside stations were rail company owned gift shops, convince stores, etc.
I think that connecting outlying areas (especially ones you the railroad build yourself) to department stores is what got Japanese rail companies going, but it's probably less important now than it was initially. Farebox revenue covers profitable operation of the railroad. It even appears to cover upgrades; browse around on the satellite view of Tokyo and you can see many private companies moving their above-ground infrastructure to (expensive!) subways because ... trains hitting cars interferes with their ability to earn money. It is honestly something that I have trouble wrapping my head around. The business is so good you can afford to make it better, but the business is a commuter train? Weird!
I think Japan is successful because of a less pervasive car culture than the US. People expect to walk 30 minutes to the train in the morning, that's just something you do. It would be unheard of in the US (and also dangerous in many suburbs, because they are designed to move as many giant SUVs as possible per hour, not to let pedestrians and cyclists get to the train station).
Also, a big caveat is ... all of this is Tokyo and Osaka, very large, rich, and dense cities. When you go out into the middle of nowhere in Japan (even an hour out of Tokyo, think the Hachikō line, etc.), rail service kind of sucks and is subsidized heavily.
