Actually, the number of people physically killed by a Muni bus annually is significant: IIRC, there's a small but non-negligible (single digits) number of people who are run over and killed by Muni every year.
We focus on crime, because it's easy to lash out at order breaking down and can relate to being harassed by the small percentage of Muni riders who can genuinely be considered subhuman refuse. In reality, though, SF has several times as many annual traffic casualties (around 3000, from some rudimentary Googling) as crimes reported on Muni (around 1000).
That latter figure has some factors that may suggest undercounting (it's reported crimes, and I can see how people might have so little faith in Muni that they don't bother reporting it) but also some that suggest overcounting (it includes fare violations and eating on the bus).
Muni certainly needs to be cleaned up, but let's not get ahead of ourselves: you're much more likely to die via automobile in SF than being shot or stabbed on the Muni. I wouldn't be surprised if you're more likely to be killed being hit by a Muni than murdered on the Muni.