Before doing this trip we searched for relevant information across few forums, we found few very helpful and we decided to post our updated description, hopefully it will make your journey easier.
In order to make the trip in one day, one should arrive to La Ceiba (the port city where the boats leave to the islands) before the last ferry leaving (16:00 for Utila, 16:30 for Roatan). This cannot be done by public transportation. It can only be done with shuttles arranged by the hotels/travel agencies, leaving at 07:00 from Puerto Barrios. Prices are: 280 Q for the one arriving San Pedro Sula (the shuttle will drop you off in time to catch the bus to La ceiba), 400 Q for the one arriving direct at La Ceiba.
We’ve done the trip in 2 days, using public transportation and 2 taxis when we couldn’t find any.
All prices are current to May 2013.
First day - From Livingston
Take a speedboat to Puerto Barrios, 35 Q, 0.5 hour, you can also take the ferry at 06:00, 20 Q 1.5 hours.
Take a taxi to the market (where all the minibuses leaves from), 15 Q (for 2 persons), 5 minutes
Take a shuttle to the border, 20 Q, 1 hour
Entrance tax in Honduras is 3 USD $
Take the bus to Omoa, 60 L$ for the direct bus, 0.5 hour, 45 L$ for indirect bus, journey should be take a little bit more than1 hour
Spend the night in Omoa. You can also spend the night in other cities on the way but from our research this little village looked the nicest (we spent an extra night here).
On the Next day - from Omoa
From Omoa take an early the bus (we left at 6AM to have a lot of spare time) to Puerto Cortes, 19 L$ 1 hour
Take the direct bus to San Pedro Sula, we took Impala, 52 L$ 1.5 hours, we had to pay extra seat for our bags.
Take the bus to La Ceiba, we took Diana express at 10:30 to get on time for the ferry for 115 L$, 3.5 hours
Take a taxi to the ferry, 70 L$ (for 2 persons), 10 minutes
Ferry to Utila – leaves at 16:00, 25 US$
Ferry to Roatan – leaves at 16:30, 30 US$
Enjoy the journey!