Also, Clipper cards have been around many years. They aren't a recent addition to BART.
Assuming a value system in which certain acts are wrong even if not observed / punished, some acts can be rational _and_ malicious.
(This isn't intended to say anything either way about BART's actions here, which are obviously not the same as literal robbery; I'm mainly disputing the idea that rational acts can't be malicious.)
Having worked in, for, and around governments, this was almost certainly an oversight that hasn’t been a big enough of a fire in comparison to the other fires.
Making a public stink about it makes it a bigger fire though, so the system is working as intended!
by taking money from those weaker than it, since it is a large well financed organization and the people riding it will not be equipped to fight it (legally), that's malicious.