Macbook Air's are much tougher than conventional laptops/netbooks. I've been touring with mine (13" version) on/off-road with the bicycle and motorbike for over a year. I just use a Thule Gauntlet sleeve, and the laptop's not got a scratch.
you really don't need to go nuts on padding, for the metal-cased/no-moving-parts Air. In the middle/top of the topbox is a good idea, without any heavy items on top of it. And you need to keep it waterproof on the motorbike, maybe just put it inside a zip-lock A4 wallet (which adds almost zero bulk).
Far more fragile are the cables. I use a plastic food container which has a snap-lock lid, which protects all the cables I need (and stops the plugs damaging anything else).