Make sure you are using a slo-blo fuse in the circuit. Sounds like you may be using a quick blow fuse. A DC motor looks much like a short circuit at startup until the motor spins up. After that is settles out and all is well. What the fuse will "see" however is the intital short circuit current spike followed by the normal operating current. The slo blo will allow the fuse to hang in there until the spike is past while the quick blow will not.
