My son (who does not have CF) needed nebulizer treatments as an infant due to a nasty illness. He hated them and was screaming pretty vigorously throughout the treatments. As hard as it was to cope with, the hospital staff was very reassuring, telling me: if he's crying, you know he's getting an especially effective breathing treatment due to how deeply he's breathing! It didn't make me like the crying any more, but just knowing that made it a little easier for me to cope with what I felt like was torture to him. He didn't need too many treatments so never had to get 'used' to them as the kids here do... but as others have posted, it does become routine in time so hopefully he will soon be able to tolerate them better.
It is a common thing for babies to have trouble with loud noises; if this is a particularly big issue with your son I wonder if running the neb while not using it periodically with him in the same room can help get him acclimated to the noise. We also sit ours on a folded towel so vibration against the table doesn't add to the noise and keep it as far away from Emily (my child w/ CF) as the tubing will allow (it drives her nuts and ours isn't even that loud!) I'd be careful not to block the air vents or filter on it, though, if trying to muffle the noise with something on or over it.
It is a common thing for babies to have trouble with loud noises; if this is a particularly big issue with your son I wonder if running the neb while not using it periodically with him in the same room can help get him acclimated to the noise. We also sit ours on a folded towel so vibration against the table doesn't add to the noise and keep it as far away from Emily (my child w/ CF) as the tubing will allow (it drives her nuts and ours isn't even that loud!) I'd be careful not to block the air vents or filter on it, though, if trying to muffle the noise with something on or over it.