How can I get my baby to better cooperate (stay still) during breathing treatments?

Distraction. Anybody who has done a nebulizer knows it's a noisy, scary thing. It vibrates, and sounds like a jet engine. Plus there's steam, and while all this is upsetting the baby, you're going to go cover her face with it. Most babies will calm after awhile as they realize when all this happens their breathing gets easier, but at first, simple distraction is the only trick, with music, tv, puppets, etc.
Not easy. Discuss the problem with your doctor. Sometimes using a spacer with and appropiate sized mask is an adequate solution and a lot easier on your nerves!