I have a 55# MK All Terrain on the bow of my 14' fisher jon boat.  We used it for most of the day on the #1 setting then decided to use it on #5 to head back to dock.  After about 2 minutes on 5 speed the motor clicked off and smoke came pouring out of the inline fuse holder.  We burnt a hole right through the 30 AMP fuse.  We use 10 GA wire and a 27 group deep cycle battery.  Any ideas why the fuse just didn't trip?  I have my batteries mid boat so the wire run isn't more then 6 ft.

Probably because the motor was trying to pull about 45 amps through your 30 amp fuse, usually does it everytime.

First you need to throw the whole fuse setup in the trash and get you a 50 amp circuit breaker.

Then you need to take that #10 wire and have it recycled.  If you are only running a few feet a #8 might work but you really need to go with a #6.