I've never traveled alone, but I would expect that if you use the same common sense that you would in any American city, you'll be fine. We've only ever flown from SPS to Ceiba, but I've heard that the busses are actually pretty nice, especially if you spend a small amount more for the first class ticket. There's one called Vianes Transportes and another is Alas Hedman (or Hedman Alas, I forget, and my spelling may be off.) They both have several departures to Ceiba each day.
If you already speak some Spanish that will be a help to you, but we speak very little and have always managed somehow. As to getting to the Bay Islands, there are flights, but the most economical way is the ferry (one goes to Utila, another to Roatan, I don't know much about Guanaja, but someone else can probably tell you). We love taking the ferry actually, and you'll be perfectly safe on it.
My only caution would go back to the same "common sense" idea. I've heard that San Pedro Sula is not a place that you want to go out and about at night. In Ceiba, Hubby and I have often walked after dark, but have also been cautioned about that sometimes depending upon how late and where we're going. I definitely don't think that I'd do it alone. Taxis are extremely plentiful and pretty cheap, although they get more expensive as it gets later at night.
I hope you enjoy your stay in Ceiba...it's one of my favorite places, and don't miss the bay islands! I'll try to help if you have any other questions.