Fuses and breakers are generally to protect wires from overload and prevent overheating or fires.
Fuses or breakers should be used at any point a high current power source splits to lower current wiring.
You can also add fuses for different sections of a PLC systems, eg. one each for the PLC itself, one for local inputs, one for distant inputs, one for local outputs one for distant outputs etc etc.
They can make future faultfinding much easier.
(By local, I mean the operator panel or control panel the PLC is in, distant being switches and sensors around the machine being controlled).
AC power Surge protection is done using purpose made filters or VDR based modules.
Control and signal line protection is by proper wiring layout and screening where appropriate, keeping all low voltage wiring physically separated from power wiring (eg. separate steel trunking for low voltage and power cables) and proper suppression of all inductive loads, both such as relay and contactor coils and AC loads such as motors.
Cables from high frequency inverters / drives to motors should also be screened.