Spoiler warning: Plot and/or ending details follow.
A safety protocol is a protocol designed to protect the health and safety of individuals.
Safety protocols were in use on starship navigation systems in the form of oversight processes, which helped stabalize the ship in the event a pilot lost control of the ship. (DSC novel: Drastic Measures)
Such protocols were heavily in use in holodeck technology to prevent users from being injured or killed by a dangerous condition in the holodeck. A computer malfunction, however, could disable such protocols. (TNG episodes: "The Big Goodbye", "A Fistful of Datas")
After becoming angry in a Borg attack, Data tried to recreate the emotions on the holodeck, and requested Geordi LaForge help him disable the safety protocols to ensure the holographic simulation was as realistic as possible. (TNG episode: "Descent")