There are a few factors to take into account if you fly via San Pedro Sula. First, the cost of flights and checked baggage (and maybe the ferry). Second, the extra time to make the hop(s) to Roatan. If your flight into SPS is late, you may need to spend the night there. Third, the risk you have with your baggage getting delayed or lost on a local carrier. Even if all you have is a carry on bag, you may be told to check it on a puddle jumper plane since those planes sometimes have weight restrictions so one of your bags may not arrive on the same flight as you. Also, in Roatan, the airlines do not bring your baggage to your hotel if it is delayed. You will have to call the airport and may also have to pay for transportation to and from the airport to get it.
I am not saying you shouldn't fly into SPS. Just make sure you look at the whole picture.
I am not saying you shouldn't fly into SPS. Just make sure you look at the whole picture.