But people also want public transport in rural regions and there it is just far way from profitable. But it‘s still necessary to provide IMHO.
https://asia.nikkei.com/Business/Transportation/Tokyo-Metro-...
"The company recorded a net profit of 61 billion yen ($560 million) for the year ended March, up 0.6% from the previous year thanks to external factors such as the increase in foreign visitors to the Japanese capital. It posted revenues of 435 billion yen."
I don't think there's something fundamentally different about Tokyo compared to other dense metropoles like NYC or London. Low density cities like LA might be a different story.
As others have pointed out, there is. It's about owning the land where you set up your stations. You don't make money on the tickets themselves, you make money by charging rent to companies in highly convenient locations.
Some European cities do this on a smaller scale (like a shop or two right at the station), but nowhere near as much as they do in SE Asia.
But it's still pretty unfair if you think about it: having a subway system is a major plus for a city, so landlords get to collect more rent (generally, and even more if the building has a subway station nearby). So it's only natural to ask them to pay slightly higher taxes to help finance public transportation. But subway systems still have to justify why they are cross-financed using tax money...