The Protector Program was a Machinist Program (in the form of a human female) whose role of monitoring the Matrix was not explicitly explained. Even the Merovingian did not seem to know about this program. When Agent Pace was asked that question, she said that she had "no clearance to address the matter". It is said that she can blend in among the humans.
She was last seen with the Oracle, which may suggest that she may be protecting another precious program, maybe the Biological Interface Program.