Fast-forward 5 decades. Inflation is real but fares are still a nickel. The city is quite happy with this contractual arrangement, quite happy to make the railways stick to it, and quite happy to take over their operations once they fail. Then they started their big "IND Second System" plan to build a kajillion subways out into all the different stretches of the boroughs (including the Second Avenue Subway up to Throgs Neck): https://upload.wikimedia.org/wikipedia/commons/b/b3/1939_IND...
... and by 1975 the city was on the brink of bankruptcy too.
As for mass transit in the modern era, it's certainly not surprising that it's unprofitable given who's operating it. Profitable mass transit is surely impossible today... politically, anyway. :b
The real MTR strategy, though, is that they get to choose where stations go. That allows them to buy up land in the area, before they announce a train is going there. The land next to the train station suddenly skyrockets in value... and the MTR make out like bandits.