Transit conductor assaults are an epidemic, as is farebeating, panhandling, etc. This can make transit unpleasant. Which is why I like proof-of-payment: while checking fares, cops can also walk the vehicle to police bad behavior.
A lot of good points made by that article that I had not considered. What happens to homeless people who are caught fare-hopping? They get a fine they'll never pay or they're put in jail/prison? I think that's important, particularly in cities where light rail is struggling.