Couldn't I just run a 50 or 60 amp fuse instead of a circuit breaker. It seems it would be just as effective protecting the motor, just would need to carry extra fuses.
What engine do you have Merc, OMC, why would you want to change out a circuit breaker and put in a fuse, did it go bad? You can do it as the older OMC's had 50 amp fuses in them.
Either one works. However you need to determine whether you need a 50 or 60A. 60A fuse in a circuit with wire sizes too small will cause the wires to melt before the fuse blows. If you have a 50A breaker now, do not replace it with a 60A fuse. In my view, a breaker is a better choice for a troller since the motors tend to get bound up periodically with weeds or stalled in shallow water. Once freed they will run again after the breaker is reset. It is assumed however one is smart enough to turn the motor off before untangling it so you don't shred your fingers in the process. Those high loads will generally blow a fuse quicker than a breaker so it could be an annoyance to replace a fuse just because the motor had a sudden high load the fuse couldn't handle.