LA's metro, like MTA, also currently has fares and doesn't keep out the homeless, as fare enforcement here is a complete joke, so i hear what you're saying. i think the point was that being unvalued would mean that people would be even less likely to do or say anything about it, and it spirals into an even worse tragedy of the commons situation (the unintended consequences).
i'd personally like to see metro raise base fares, and provide larger discounts to lower income riders via their LIFE program to offset that potentially regressive burden. in the best of times (before covid) fares only covered about 20-30% of operating costs, i believe.
use that money to implement better service (more and more punctual trains), more social/community officers to help the homeless, peace officers on the trains themselves (currently they mostly just walk around stations every once in a while), and more rigorous cleaning and general maintenance.
this all needs to be coordinated with getting housing and services to homeless folks, removing roadblocks to density along transit corridors, and emphasizing multi-mobility (like converting street parking to bus & bike lanes).