I brought my maltese Codie on a plane w/ me before. What I did was put a wee wee pad on the bottom of his bag (in case of an accident) and half-way through the flight I took the carrier into the bathroom on the plane and let him out for a minute. Then I gave him some nutrical (to keep him from getting dehydrated), checked his pad (which was dry as a bone) and put him back in. I stayed in the bathroom for about 15 minutes so that he could stretch and go pee pee on his pad (I put it on the floow of the bathroom) if he had to go. When we stopped over to change planes I took him to a bathroom and let him out of his carrier. He went pee and then we boarded the next plane. Again, after about 45 minutes I took him into the bathroom to let him out briefly. He was perfectly comfortable and ok w/ flying. On the return flight, the flight attendant let me hold him under my blanket.
I think the best thing to do is get them used to being in a carrier so that they are not frightened on the plane. Also, give them a small toy or a bully stick in case they get restless. Codie basically slept for the whole flight. I am traveling to visit me in-laws again in December and now I am bringing my new dog Katie (she is a Yorkie). I hope she does as well as Codie did. At least she will have him to comfort her if she gets scared.