We
don't use accounting (fares) to plan local public transport, at least not exclusively as it's not at all a reliable, what with its inability to track routes, lots of unregistered riders with monthly tickets, etc. etc. To get reliable data, you need to count people in the vehicles and poll them regarding their route and other things -- which of course the public transport authorities do routinely. Automatically tracking people is an invasive technical improvement to this, and it's deployed in some places, but again it doesn't really require fares.
Trains of course do require additional staff to handle higher loads, as do all modes of transportation, but with trains the staff/passenger ratio is ridiculously low, and it gets lower as they are used more. Of course there's a resource allocation problem there, but again, fares don't seem to be very useful there, at least in the realm of local public transport.
Charging money does limit the ridership, which was GP's point, and which is the opposite of what sensible minds would want, namely less cars on the roads. Vandalising trains carries with it much harsher penalties than free-riding, so I doubt fares are a very effective deterrent; you don't need to pay a fare to spray a tunnel wall, just a disregard for the law and maybe your own safety. Other people you might describe as bad actors might be affected by fares, but I'd hold that if homeless people have no better recourse than abusing trains, you might want to solve that problem instead of making it less publicly visible.