Most communities of any size have a local taxi system. They're ubiquitous and usually reasonably priced. In Tegucigalpa and San Pedro Sula, where the city bus systems are not safe for foreigners to use, and where driving your own car and finding parking can be a real a hassle, taxis are the perfect motorized alternative for getting around. In the capital and San Pedro, as well as La Ceiba, taxis should be your only option for going anywhere at night. Have your hotel call one for you if you're going out after dark. Likewise, when you're ready to call it a night, have the restaurant or nightspot call you a cab rather than you hailing one on the street after dark. It's safer that way.
In bigger cities, the taxis are regular sedan-type vehicles. In smaller towns, such as Copán Ruinas, the taxi system will be a fleet of semi-open, three-wheeled, motorized Bajaj vehicles made in India. Everyone refers to them as tuk-tuks. (The name echoes the sound of the engine.) They're great fun to ride in for short distances, but can be noisy and bumpy.
Taxis are not metered anywhere in Honduras. Agree on a fare when you get in. The amount is generally reasonable. Roatán taxi drivers have a reputation for overcharging tourists. Ask the friendly folks at your Roatán hotel front desk to give you the lay of the land and to tell you what reasonable fares should be.