We specifically flew airtran as they charged $75 per dog (the others wanted about double. The higher priced airlines also wanted a health check up, shot records, etc. (even though I had a recent health exam, and everything in order...I didn't want to miss something at the last minute and then what do you do??).
The size of the carrier also had to be a certain size and they give exact dimensions...very small! There really is very little room for the dog to even move around