Not all antagonists are fire breathing Card Carrying Villains, a good many are Plucky Comic Relief Harmless Villains, or just plain incidental annoyances, and these guys just can't be done away with using the same response as the former. It just wouldn't jibe to have a hero beat said antagonist to within an inch of his life for putting itching powder in his cowl, at least not without the hero being an Anti. In that sense, the Karmic Protection extends both ways: it protects the annoyance from real harm, and the hero from karmic backlash as he's perfectly justified in his response.