I can't claim to understand Muni's problems, but it occurs to me that an train is a much simpler problem (technically speaking) to solve than a self-driving bus. The former doesn't have to flow in and out of unstructured traffic, has only one degree of freedom, has well-deployed reference systems, etc.

Maybe one day we'll have fully automated buses without any operators at all, but for the time being my understanding is that even self-driving cars still need a tender. The kind of bus volume (and corresponding idle drivers) you'd need to make up for a train's worth of commuters probably takes a heavy cut into any operator labor savings.