There are many ways to get to Honduras.  They probably include flying into Tegucigalpa or cruising along the Caribbean until you arrive in San Pedro de Sula.  I really don't know for sure about those methods.  I've only been in and out of Copan Ruinas, which is just a few miles from the border of Guatemala.  It's an easy border crossing and the police on the Guatemala side are especially helpful. (To understand that fully, you'll have to read my adventure.)

Once you enter Honduras, there is a little parking lot that serves as a terminal for vans and trucks that can take you on to Copan Ruinas.  It's surprisingly easy to do. And, since it really is a short ride, no matter how crowded or uncomfortable, it isn't going to last very long.