For MTA: labor expenses are higher than revenue, there is no easy way out.
Cities with expensive transit typically have mandates that x% of costs must be paid by fairs. In Wellington, NZ and Chicago, US, this is 50%, leading to some pretty high fares or low service.
Just having transit makes revenue though, in taxes from the increased commerce. Access to transport is also the single largest factor in escaping poverty. It's difficult to measure those numbers in revenue though.
But transport always must be subsidized by the State, going back to the roads of Rome.
Since this is not the case in NYC and Chicago - private individuals / the city owns the property adjacent to transit, there needs to be some other way to capture that value. Enter a sane, necessary taxation / subsidization mechanism.
* The value is real. Property adjacent to transit was insulated from the 2008 crash: https://usa.streetsblog.org/2013/03/22/study-homes-near-tran...
Ironically many car drivers object to the public subsidy of rail, arguing transit should never be publicly subsidized.
Your link seems to prove the opposite. It says that Colorado has the 24th largest share of roads paid for by gas tax, tolls and user fees with 49.9% paid for in that manner. That means that only 23 states have a majority of road spending paid for by gas tax, tolls and user fees, so most states (>50%) have less than half of road spending paid for by gas tax, tolls and user fees.
Once the rail lines are paid for, the cost per passenger is very low. Hence, we should maximize value by making it free.
Once the rail lines are paid for, the cost per passenger is very low
You also need massive capital investments into the rolling stock and all this requires significant maintenance.
An argument can certainly be made if public transport should be free, but stating that the costs are low and essentially paid for once the (very expensive) infrastructure stands is just ludicrous.
If that were the case, the whole reason for this article wouldn't exist, because NYC wouldn't need any maintenance for its subway system.
This is demonstrably false. There are plenty of systems where fares make up close to 100% (or even exceed 100%) of their costs with fares: https://people.hofstra.edu/geotrans/eng/gallery/Map_World%20...