I deal with this issue on an almost daily basis! It's tough to get to Utila... Anyway, for most people flying into San Pedro is the cheapest option when coming to Utila. Use Frank Morgans Travel or Alice's Worldwide Travel to book flights from San Pedro to La Ceiba, then on to Utila.
Morgans Travel Agency- Utila, The Bay Islands, Honduras
World Wide Travel - Utila, The Bay Islands, Honduras
You'll find contact details on those pages, they both speak English and both been organising flights on and off the island for years. Don't bother trying to speak to SOSA, it's basically impossible.
Utila is too small to have a flight everyday. So if there is no flight available on your day of travel take a cab to the ferry terminal and take the 1 hour ferry crossing. Or if you really want to fly there are charter flights available, again talk to the Utila travel agencies for details. I think the cheapest one takes 3 passengers with not too much baggage for around $180 total. The flight takes about 10 minutes! Scheduled flights with SOSA are $55 per person, one way, if I recall correctly.
Utila's airstrip has developed a little. There is now a proper building with a bar, etc but unless a scheduled flight is coming in it is probably closed. Making sure you have a pick up is important if you want to be sure of avoiding a 2 mile walk into town.
There are only charter flights available from Roatan to Utila. Captain Angelo does it regularly with his 10 seater at $112 per person last time I looked.
Guanaja Air
9558 8683 cell
lagonia@aol.com
If you would like any more information about travel to Utila, diving here, etc please feel free to PM me!