The free fares remove the non-negligible cost of fare infrastructure and enforcement, plus the general in-person friction created by the need to pay (queuing; hunting for cash; etc.). Worth considering the hidden expense of the status quo and weighing against the alternative.

There's a similar issue with bus stop consolidation, where the bus runs way more efficiently when stops are removed, but mobility-impaired individuals are left out in the cold.

That is definitely always considered!