Ashley,
Just a few thoughts to add to this subject. I have never really heard any valid argument against using skids. Bryan makes a really good point about a skid actually being protection against a forklift, so in a sense this is a sacrificial layer as a skid can always be replaced. As to truck vs. plane, you must keep in mind that an airplane won't be picking up a crate at your museum so even if it goes on a plane you are still sending it on a truck two times. The truck that will be picking the crate up to go to the airport will normally be a bob-tail type with a short wheel base traveling over less than perfect city streets. Even with air-ride, it will get a much bumpier ride than in a tractor trailer.
More importantly, when you send by air you double the number of times that the object is physically transferred, and that is statistically the most dangerous period of transit so it is worth thinking about. By truck even if you don't purchase "exclusive use" it still won't be loaded and unloaded those two extra times and it gets a better ride while it is on the ground.
Regards
Kurt