The last time we flew Airtran we had an early flight into Orlando (non-stop from Pittsburgh). I checked a few weeks later and the flight had changed to a late afternoon arrival. By the time we actually boarded the plane, it was back to it's original time.
If you have the time, I'd just play the waiting game. If you book quite a bit in advance, your chances of it changing are pretty good - and that goes for other airlines as well.
We're flying to New Orleans and we had a straight flight (again out of Pittsburgh) but in checking, it now has one layover in Charlotte and get into New Orleans at 2:45 instead of the original 12:30. It may change again - who knows. I guess that's the price we pay to get cheaper air fares.
I agree that a 6 hour layover with small children is unthinkable. Hopefully they'll either change it back or you'll be able to do something different. It doesn't hurt to call.