Can I use the list on a Ruin Runner?

No. The List's activated ability requires choosing a specific unit with the named tag, which counts as targeting that unit. Since Ruin Runner has "I can't be chosen by enemy spells and abilities," an enemy cannot target it with The List's ability.

This isn't a programmatic selection (where no choice is possible) — the player actively chooses which unit with the tag receives the effect, so it's a target (Rules 355.10, 355.10.d). The protection applies.