I like the sibling comment idea of using AI eventually.
But in general for public transportation I think running at a loss is not unreasonable. It's nice if it's profitable, but it's ok if it isn't. Hopefully it's reducing emissions, giving people who can't or don't want to drive reliable access to their employment, etc. is still worth it.
this is a problem that autonomous driving could fix more easily than the general driving problem due to the fixed route, but good luck having the bus driver union not throw rocks at your AVs