Because urban New Yorkers are paying for rural areas' transportation infrastructure. In fact, state taxation and spending policies represent a large net transfer from urban areas to rural areas.
An old lament. Why should rural (anywhere) fund the city folks' needs? E.g. Here in rural Iowa, we pay state taxes for schools like everybody else, and have a tiny underfunded school vs the nearby city's grand edifice with two theatres, enormous football facility, AP classes and full staff.
In most cases it's the city folks subsidizing the rural folks. It turns out that it costs a lot more money to build the roads, power lines, schools, etc than the small number of rural residents that benefit from them will ever pay in taxes [0]. And in the specific case of New York's MTA, revenue from subway fares has repeatedly been diverted to pay for things other than the subway [1].
Everybody benefits from farm access to markets. Rural roads are there for everybody. To say 'its more money per capita for rural folks' just means you're using a heatmap of population and putting it over infrastructure - shazam, it doesn't match!. But it says nothing about who's getting the utility out of the infrastructure.
