Pretty asinine of him to back off at that. Homeless people aren't paying fares already. There are also 60k homeless in LA while 1 million people ride ride metro a day; even if every single homeless person boarded metro one day it would be a blip on your radar compared to everyone else.
What fares hurt most are the working families in LA who pay $76 a month to ride the bus to work or school because there is no other choice. The fact that Newsom didn't connect this dot doesn't surprise me.