Yeah, as wealth generation becomes more urban you have to pretty much expect cities to subsidize suburbs and rural areas.
The main issue here though is that due to some sordid political history the MTA is a state agency, despite running the NYC subway. This has resulted in the city's transit budgets being routinely raided to supplement state budget needs, and also a focus on state-centric mass transit efforts to the detriment of in-city mass transit (see: redeveloping Penn Station which serves long-distance train commuters, designing the AirTrain to LaGuardia to primarily serve suburban Long Island travelers, etc).
There's a pretty dramatic misalignment of incentives when a state agency under the command of the governor runs the city's subways, rather than the mayor or even a regional government.
You can get the BART problem although, where you have to get 3-5 counties and 25+ municipal governments working together to make a unified metro transit system. In the BART's case, only 2-3 counties did and now there are big transit gaps everyone regrets today.
Isn't the phenomenon of money being transferred from city->country an inevitability in any society with progressive income taxes?