Okay in a recent game me and my friend are trying to figure out if skull crack also affects creatures with protection. I can't link the cards anymore at least my phone is being dumb. Say I brave the elements and he says skull crack what exactly happens
{Brave the Elements}
{Skullcrack}
Skullcrack only hits players, not creatures, so...protection is irrelevant unless you are somehow granting protection to a player.
Edit: my apologies! I just realized you were asking something else entirely.
Protection's anti-damage effect is indeed damage prevention;
702.16e (http://imtgapp.com/forum/index.php?action=imtg;area=rule;number=702.16e): Any damage that would be dealt by sources that have the stated quality to a permanent or player with protection is prevented.
So if a player is skull cracked, his creature with protection could still receive damage from the protected source. It still cannot be enchanted, blocked by, targeted, or anything else that protection stops from interacting with though.