However, it may not include the real estate income, but it does include the income from extra ridership created by the real estate being near the station.
It's true, the bullet train prints money for JR. But there are also many train companies that are only profitable because of their real estate holdings around the lines, especially smaller private companies like Tokyu.
The bullet train in Japan only "prints money" for one JR company: JR Central, thanks to the busiest(?) bullet train route in the world: Tokyo to Osaka. Most other bullet train lines in Japan are break-even or loss making, but supported by the central gov't (for social policy).
> only profitable because of their real estate holdings around the lines
Again about Tokyu: This is untrue. I could only find stats from 2005, but all train lines in the Tokyo metropolitan area (including Yokohama) have improved farebox recovery ratios in the last 20 years.
After the opening of the last Tokyo Metro line (Fukutoshin) -- with direct connection to Tokyu Toyoko line (Shibuya to Yokohama), the farebox recovery is surely much higher. I guess over 150%, but probably closer to 175%. The trains are jammed 8+ hours per day. This means that, excluding real estate development, the Tokyu train lines are profitable by themselves.
> especially smaller private companies like Tokyu.
About Tokyu: "[S]maller"? Absolutely not. It is surely one of the top 5 largest private rail companies in Japan by revenue/profits. They are huge in the Tokyo area.
However, it may not include the real estate income, but it does include the income from extra ridership created by the real estate being near the station.