Barkoutloud,
The same thing happened to me. I booked my flight with Virgin America (I heard they are not as strict with dogs on board), it was $50 extra charge for the dog and than I couldn't find a carrier my little mutt would fit in.
After hours of research online, I found a product called Sturdibag. Check it out!
www.sturdiproducts.com I love my sturdibag. I got the medium size and didn't have any problems getting it on the plane. Mine is black, so most people didn't even realize that I had a dog with me
Good luck!