Besides the motor scooter three wheelers so commonplace in Honduras, there are also pick-up trucks to transport people and luggage around the island. We found two scooters more expensive than the pick-up for hauling our bags and ourselves around the island, so bargain hard.
Boats from Coyolito tend to drop off in the afternoon at the main port in Amapala, but often it's easier to catch a boat from another beach a mile south of town. Ask the hotel about this to clarify the details. Price to and from Coyolito by these boats is the same rate. Your hotel can also arrange for pick up at the Amapala port for a trip around the island, or to other islands. There's an aduana at the end of the pier in Amapala, but it was closed when we were there.