My understanding of how Japan transit is profitable (I live there and I'm interested on it quite a bit) is multi-sided, but the main difference is that train companies own (or are leased for free/cheap) the station areas. So they setup big malls and stores around the stations, that for the fact of being on a station are probably the most transited and profitable ones in the nation.

Some smaller but meaningful differences might be that Japan urban density is very high (small country, lots of mountains/forests), that there's a lot of public transportation traffic, that the train rides for employees are normally subsidized by the companies, etc.