No, it will not. Protection only prevents a permanent from being targeted, enchanted, equipped or being blocked by a source whose property it has protection from, and also prevents all damage dealt by that source. Since Supreme Verdict doesn't target and doesn't deal damage, it overcomes protection.
Protection from X means:
This object can't be dealt damage by a source of quality X
This object can't be enchanted by an Aura of quality X
This object can't be equipped by an Equipment of quality X
This object can't be blocked by a creature of quality X
This object can't be targeted by a source of quality X
Only a little correction of Epochalyptik's post.
"This object can't be dealt damage by a source of quality X" is not exactly correct. It should be "Any damage dealt to this object by a source of quality X is prevented." This is important because some spells and effects (like Skullcrack ) can help you overcome protection in cases where the damage is not targeted (overloaded Mizzium Mortars or when a creature with protection from creatures blocks for example).
Just remember DEBT. Dealt damage, Enchanted/equipped, Blocked, Targeted