Can I activate Wages of Pain from hidden to target a Ruin Runner attacking me?

No, you cannot target an opponent's Ruin Runner with Wages of Pain.

Ruin Runner has the ability: "I can't be chosen by enemy spells and abilities."

Because Wages of Pain is a spell that requires you to choose a target ("Deal 3 to a unit at a battlefield"), it is blocked by the protection ability on Ruin Runner. As established in RiftJudge FAQ #4624 and #8581, spells that require choosing or targeting a unit cannot be used against a Ruin Runner controlled by an opponent.