When pets are transported on an airline, they are put in the luggage compartment.
There is no sound proofing and no climate control. Typically this can be fairly traumatic for the animal. Also, they are basically treated as luggage, so are subject to the same issues that can happen to your underwear.
http://doglaw.hugpug.com/doglaw_042.htmlQuote:
Commercial airlines are not deliberately cruel or even particularly careless when it comes to shipping dogs; they just aren't set up to deal with pets efficiently. Unless a dog is small enough to carry on board the plane, air travel is a risky way for it to go.
The basic problem is that to an airline, your pet is just an especially bothersome piece of baggage. And as everyone knows, baggage slip-ups are inevitable, given connecting flights scheduled too close together, long delays, and human error in a stress-filled, overloaded system. When a mistake means your luggage goes to Minneapolis while you go to Atlanta, you'll survive the inconvenience. But if your dog goes to the wrong city or is forgotten on a luggage carousel, it may not survive.
I didn't quote the entire article.