I don't think that is rolled out to all locations yet. We will be leaving from Chicago Midway and when I check southwest.com they do not show AirTran flights. I really hope they do soon, because ideally that would be the way we would like to go (best of both worlds).
Or am I just missing a button to show all AirTran flights also?
When I search BUF (currently Airtran and Southwest) and ROC (currently only Airtran), flights for both companies show up on the Southwest website.