54lion, are you trying to book a vacation package? That will make a difference over purchasing separately. FYI, I think it is the hotel that takes the bite on the lower combined rate, not the airlines. Just last week I was on a flight/hotel/car rental package through Orbitz, and it showed on my cc bill with 1 line for flight, and 1 line for hotel/car combo. The flight amount was same price as if I'd booked it on its own.

For flight only, I use the searches like Orbitz to compare (or verify) best rates and schedules, then book directly with the airline.

Try looking at one-way tickets, you get better selection of the schedule you want, and the price is the same. Airtran has been good for me the last few years. Pricing has been LESS than it was a couple years ago.

PS Apple Vacations flight only brought up Airtran as my best option, and the price was $20 more than booking through Airtran...

Of course, it depends where you are flying from as to what is available for you. Good luck!