It depends on who you are flying with.
Southwest, JetBlue, Song and Independence will book each leg at the published rate for that segment, therefore what you are actually doing is booking 2 oneway tickets. I have seen no extra charge if only booking a oneway ticket.
I have done this for this April as I am driving down with my DS who is starting at AMI Daytona in April. He's staying and I'm flying back Song @ 79.00