"To protect the flock" means to take care of and ensure the safety of a group of people under your responsibility or those you care about, just like a shepherd protects their sheep from danger and harm. Full definition
They will protect their flock with great intensity and will do so without human guidance or supervision, requiring very little training in regards to protection. (animals-universe.info)
For the most part, these dogs were used for protecting flocks of sheep against wolves and bears much like the Turkish Kangal Dog. (animalso.com)