An interesting thing about Hera is that she is the goddess of Marriage. "Marriage" as defined by the Ancient Greeks, who, like most ancient cultures, defined Marriage as a man owning a woman. Also like most ancient cultures, Greek law didn't punish a married man for sleeping around. There was nothing wrong with that unless a bastard child resulted from the affair. Bastards had no place in society and were a threat to the succession laws of the time. Only a married WOMAN could be punished for adultery, because if she had a bastard, that was a threat to the husband's household.
Thus? Hera punishes the only people in Zeus' affairs that she actually CAN punish. Zeus is, technically, doing nothing wrong by the standards they uphold. The women he sleeps with? Different story. They are either married themselves, and thus threatening their own husband's household. Or they are unmarried and dishonoring whatever male family member currently "owns" them. The kids, of course, are bastards, and there's nothing wrong with Hera punishing them either.
(Please note: I am not in any way espousing these beliefs as my own, I am merely illustrating how Ancient Greek beliefs shaped the perceptions of Hera's vengeance kicks.)