This is what the Froggy's guide has to say on Protectorates...

Protectorates.
Having a faction as your protectorate gives you all the advantages of an alliance and military access, and some security; protectorates don’t seem to rebel. Regions owned by a protectorate count towards your controlled region count, getting you closer to victory without needing to conquer and manage the settlements yourself. You get tribute too, which can be very considerable if the protectorate is a rich faction.
A protectorate is basically taking a faction under your wing, that faction loses her independence to you. It gives tribute and can't attack you, or break the alliance - it is basically yours. Certain loopholes in the RTW diplomacy do allow a protectorate to break it's alliance though, if a faction allied to your protectorate decides to attack you, the Protectorate may decide to leave your side.

That's a bug, said faction should have no choice in the matter.