> but doesn't common sense suggest fewer riders mean they don't need as much money?
Not necessarily. Consider: what would they cut? Run fewer trains? Reducing frequency has a huge negative effect on how convenient transfers are, which means you're likely pushing more riders away. (It can be the difference between hopping off one train and catching a new one 5 minutes later rather than 10 or 15 minutes later. Not a fun change in the middle of your trips!)
That can then lead to even less fare revenue... and you really don't want that, it's the infamous transit death spiral.
No, the MTA seems to be running with a substantial deficit right now: https://new.mta.info/budget/MTA-operating-budget-basics
Removing fare revenue would only exacerbate that as a large portion of their revenue comes from fares.