I flew with my boys 2x. They both fit in the same travel crate. We had 1 layover in Chicago and it was a 2.5 hour flight, 1 hour layover 2.5 hour flight to our destination. First time I did it, no problems at all. some attendants make them stay in the crate the whole flight, one attendant on the 2nd leg of the flight home told me if they had a leash, then they could come out because no doggy flies in a crate while she is in charge!
That was awesome! I gave them children's (or infants... not sure which one) benedryl for the flights. I also bought special crate pads that if they did pee, throw up or an ice cube melted it would immediately absorb and wick away the moisture. They did fine.
Another time we got stopped on the second leg of our flight home in Chicago. They tried to tell me I didn't pay for them. I couldn't find the receipt (the paper ticket fell off the crate) so I had to repay for them, then they made me separate them into 2 crates. That was a disaster. No amount of benedryl helped and Dexter nearly tore himself out of his crate because he was mental w/o his brother with him. Now they are bigger and I haven't flown with them in nearly 3 years. Their flying days are probably over.