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.
February 18, 2013 7:10 a.m.
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
February 18, 2013 10:58 a.m.
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).
February 18, 2013 11:16 a.m.
Just remember DEBT. Dealt damage, Enchanted/equipped, Blocked, Targeted