Often protectorate worlds are those with pre-spacefaring indigenous populations, and the protectorate status is aimed at preserving the Prime Directive and allowing the native culture to develop as much as possible on its own.
In many cases protectorates have not yet had first contact. In such cases Starfleet enforces a complete quarantine of the world, and all researchers of the native culture do so covertly. However, there are also a large number of cases where by one means or another the indigenous culture became aware of the spacefaring cultures around them. In these cases, research and trade take place out in the open, but Starfleet works to minimize the effects of contact and prevent excessive exploitation of either party.
In other cases, protectorates are planets that are currently uninhabited, but are located within Federation territory and placed under Starfleet's protection. Such a world was the site of a peace conference between the Hidran and the Klingons. (TNG novel: Foreign Foes)
Captain James T. Kirk threatened to make planet Sigma Niobe II a Federation Protectorate to protect them from the manipulations of the Redheri Trade Consortium. He later learned Sigma Niobe II was not subject to the Prime Directive. (TOS short story: "As Others See Us")
- It is probable that Bajor was technically a Federation protectorate following the end of the Cardassian Occupation, but it was never referred to on-screen as such.