Well I baught my 2 RES as babies in Chinatown NY, and flew them on over to California without a problem.
Of course this was in 1997 before September 11th... however I'm pretty sure they still let you take it on the plane with you. The way I did it (my RES were babies and I kept them in that plastic crap container they give you heh) was put a spunge andabout half inch of water in it and put it in a paper grocery bag. The lady who checked the "bag" looked at the turtles and checked to see if I was hiding drugs in it or somethign haha
Anyways my turtles are nice and healthy and didn't seem to have problems with the flight. It was really long to (NY to CA). I might not have known any proper methods to get my turtles on the plane but anywhoo they made it and I'm happy 6 years later 