There are protected batteries and "protected" batteries. They're interchangeable terms depending on who you speak to.
Many batteries have internal protection devices as part of their construction to help out in case of severe abuse. These are last ditch, permanent, protections that can MAYBE help prevent a battery from venting or bursting.
There are also batteries with small external circuit boards laid on one end of the battery and held in place with heat shrink. These circuit boards temporarily stop the flow of current in case of abuse or, sometimes, overvoltage/undervoltage situations. Almost like a circuit breaker. These protection circuits are usually limited to only a few amps max though and lengthen the battery. This makes the battery unusable in the vast majority of mods.