The issue is really that the MTA is funded and controlled by the State of New York, while it predominantly serves the City of New York. Since the population (especially the voting population) of the city is <0.5 of the state population, but the city is an outsized chunk of the state's total economy, the state uses funding of the transit system as a weapon to get the city to acquiesce to other demands.
Hence why the NYC mayor is so intent on funding worthless streetcars and ferries; they let him get out from under the thumb of the state.
