I wish they could do something about fare evasion. I ride Muni fairly often (both buses and trains), and I see maybe 20% of people paying when they get on. I know some of the remaining 80% probably have monthly passes or something and don't strictly need to tag on, but I can't imagine it's a large percentage. Biggest offenders seem to be out-of-towners who are going to Chase Center or Oracle Park events (I live in the Dogpatch and see a lot of that on event days). There's no excuse now that the fare terminals accept NFC credit cards too (and not just Clipper cards). I expect getting more people to pay could solve some of these funding problems, or at least make them less severe.
(I do wonder if the cost of fare enforcement exceeds what they'd recover in fares, though...)