If there is a short, the breaker pops and keeps the charger and battery from exploding and lighting your boat up like a 4th of July bonfire. Should be a 50A breaker on every positive lead right before your batteries, unless you have something that draws or adds more than 50A (huge battery charger or trolling motor), then use the correct size breaker.
Note* a breaker does not remove the need for each item to be properly fused as well. The breaker is just to keep from having a boat fire because of a direct short in your wiring due to rubbing, mice, heat melting wires, etc.