In general, commercial airlines are not very good to trust the transport of animals to. When pet stores and pet owners use commercial airlines to transport pets, it isn't unusual to see animals die. On most commercial airline flights, your pets don't get to travel in the cabin. They only get to travel in the hold where there is no real protection against pressure changes and temperatures changes. Not to mention, it isn't just the flight time that you need to worry about. From the time you give your pet up at the counter, your pet is on his own. It can take quite a while for them to put your pet on the plane and then bring him back to you at the other end. In other words, most commercial airlines aren't really pet friendly airlines.
Pet Airways is certainly one way to go. This is the only airline out there that's completely designed for pet comfort. It's an airline that only takes pets - not people. When you check your pet in on this airline, they treat your pet like they would a minor child traveling alone on a commercial flight.
The flight attendant takes charge of the pet, personally transports him into the cabin, feeds him and gets him some water every now and then, and keeps him entertained. If you have large dogs like Great Danes to transport, commercial airlines can be torture to them. A dedicated airline like Pet Airways is the only one that will allow him to stand up at full height instead of sitting down all scrunched up in the cage.
But there are other pet friendly airlines out there, even if they are commercial ones that transport people. Since Pet Airways only goes to a dozen cities around the country, if you're going anywhere that this airline doesn't go to, you're completely limited to commercial airlines.
Which are the most pet friendly commercial airline companies in the country?
JetBlue actually has a pet transport program that they call JetPaws. They have all kinds of allowances that allow pets to travel safe and in comfort. They allow pets in the cabin in a special section. Frontier Airlines does the same. In fact, of all the commercial airlines out there that allow pets in the cabin, Frontier allows the most. On each flight out, they allow 10 animals on board for all passengers put together.