"I wouldn't call it _malice_. I make more money robbing travellers on the King's road than not doing so, and it's very unlikely I'll get caught!"
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.)