It is possible that the software is trying to get you the options with the lowest possible fare, and the connecting flights might be the flights with a lower class booking code = a lower fare. I have booked on CO, and it has suggested as an initial routing (with no special twaking on my part) BOS-EWR-CLE-ATL...because those flights had a booking code (class of service) that was less expensive than a 1-connection flight. The computer is supposed to search all combinations, and give the customer the lowest possible fare. You could book this long routing, and if you don't want to fly it (it is extra miles!) when you check in at the ATO (airport) just ask the agent to re-route you on a direct or 1-connection flight.