There is a long time since I was there, but first of all, Central America is a great place to drive a bike. The last trip I did was 35000 km, on a xt 600, from LA in the North to Panama in the south, and return. People are truly nice, and if you need, they have good mechanics all over.
The city you are referring to in Honduras is called
La Ceiba. Its a nice medium size town on the coast, with the general problems of crime and drugs.
There was no ferry-crossing over to Utilla, most people are flying, and it takes about five minutes. :-)
I kept my bike in the Dutch guys place on the beach, but dont know if it still excists, or how safe it is.
If you go there, have a couple of

s on the Bucket of Blood. Love the place.
Cheers
Haakon