Several EU cities have experimented with making public transport free, and people seem to really enjoy it.
Also, as you so eloquently put it, it isn't clear that the cost for issuing and checking tickets is covered by the income from the tickets, and there are reasons why MTA tickets cannot be priced at the actual cost to cover the ticket compliance infrastructure -- with a nice analogy to the cost of parking vs value of parking real estate. What justifies the subsidy for on-street parking?