In SF, BART is pay-per-ride throughout the system, while MUNI is proof-of-payment in many locations. One thing that I've noticed is that there are significantly more homeless people on MUNI than on BART. As a rider, this negatively influences my experience and desire to ride (mostly because of potential for screaming/attacking).
Especially if public transportation is free, I can imagine that the homeless would take shelter there in case of inclement weather. Not a huge issue in SF, but comes into play in other cities.