Comayagua is about 2 hours by car or bus from Tegucigalpa, where the nearest international airport is located. TACA, American, and Continental airlines service the Tegucigalpa airport.
Further away, but on a better road, is the San Pedro Sula airport, the busiest in Honduras.
Rent a car at either of those airports, or catch one of the many busses running the SPS-Tegucigalpa-SPS route.
Taxis abound. Fares for anywhere in town, before 6PM, are 20 Lempiras per person. Rates go up after 6PM and again in the evening hours. Rates may even be higher at 3 AM or so. ALWAYS ask the fare before entering the cab.
In the central square of the town sits the Cathedral of the Immaculate Conception, an outstanding example of 18th-century colonial architecture.
Restaurante Casa Colonial (Colonial House Restaurant), Parque Central (next to the Cathedral). Very good food at reasonable prices in a romantic setting, on the central square, right next to the cathedral. Seafood, steaks, salads, chicken and plato tipico. Coffee shop attached. Also serves breakfast. Inquire about off-menu items such as crab, or sushi-maki. Ricardo, the owner, has filled the restaurant with art, crafts, and antiques from Honduras as well as the US. Credit cards accepted. Outside seating on the parque. Special seating for groups up to about 25.
Restaurante Toritos (Toritos Restaurant), CA-5 (On the main highway, just south of town). Toritos is probably the best restaurant in town. Known for their excellent steaks, they also serve seafood and chicken. Full bar, credit cards accepted. Secure parking.
Fast Food Restaurants, CA-5 (On the main highway, between the old and new boulevards). On the main highway, between the two major intersections, is a Pizza Hut, a Burger King, Dunkin' Donuts, Baskin Robbins, and a Pollo Compenero. Wendy's is about a quarter of a mile towards town, on the "old" boulevard. Go towards town at the Texaco, you'll see it on the left.
Golosinas. These small, inexpensive, family-run restaurants serving typical Honduran food and either fried or rotisserie chicken are on every block it seems. Food preparation in Honduras is not tightly regulated as it is in the US, but after being in-country for a few weeks, you should be able to eat pretty much anywhere.