I live in a place with a functionally free bus line. I thought it was great and used to ride it all the time, but then the local homeless figured it out and now every time I get on, the seats are covered in filth and there's usually someone who smells absolutely vile. They don't get on to go anywhere; they get on because they have nowhere else to go. They just hang out on the bus.
Obviously the real solution is to give homeless people a proper place to stay, improve mental health care, and all that good stuff. I hate the cycle of moving people from once place to another. But in the meantime, making bus lines free can make them a horrendous experience for everyone else.
Edit, also the solution to the article's actual point of fairness in fares seems simple to me. Make it free and just have a progressive tax that pays for it