Πόνος means toil or suffering, while πονηρός, derived from it, can mean either that someone toils under oppression or else is knavish, base, or evil. What is the semantic link between toil/suffering and evil? If I had to guess, I could come up with two guesses:
(1) Noblemen are ἀγαθός because that's the natural order of things, and for similar reasons, people who do hard manual labor are knavish, base, or evil for the same reason. OK, the bronze age is before any notion of the nobility of labor, but they certainly had the concept of a reliable servant, or of a character like the swineherd Eumaeus who virtuously cares for the disguised Odysseus, thinking him to be a ξένος.
(2) Maybe evil people cause suffering for the rest of us good people. But this also seems weak, since there is nothing inherently evil (in the ancient world) about causing others to toil or labor. Is the idea that πόνος specifically implies that the toil or labor is unjust, and therefore anyone who imposes πόνος on us must be bad? I suppose then we would have to have had an expansion of the word's meaning, from evil-because-they-inflict-unjust-toil to evil in general.