We have a nebulizer because last year both of our boys (at the time they were just over 2 years old and 6 months old) had RSV. The cases that season were bad and landing babies in the hospital, so our pediatrician was pretty aggressive, especially with the little guy. Our younger boy ended up with ongoing wheezing, horrible coughing fits, coughing up tons of sticky mucus, and I basically had to stay home and nurse constantly. We were referred to Pediatric Pulmonology, where they diagnosed childhood asthma. I think there is always a difference in diagnoses and communication because even now my pediatrician (whom I also adore) will simply say that our child has a tendency to wheeze, especially if gets sick, but we continue to follow-up quarterly with the pulmonary. We do maintenance treatments with an inhaler/spacer (he is now 21 months old) or the nebulizer, depending on which he will cooperate with better, and just add in albuterol in addition to pulmecort if he is actively wheezing. Some of it could be seasonal or environmental. Last year (in the diagnosing stage) they had a chest x-ray done for our little guy so they could make sure it was not pneumonia or anything, and looking at that helped the pulmonologist. My 3 1/2 year old seems to now have a tendency to get croup, but we treat him with the nebulizer, steamy showers (just hanging out in the bathroom "drawing" on the mirror, not in shower), etc. Whatever the actual condition (asthma, allergies, etc.) your treatments will probably be the same, but you might ask for a referral if this is an ongoing problem.
For now, try some environment adjustment--check his room for moisture/mold, if you have a lot of pollen, keep windows closed in his bedroom, etc. A lot of children grow out of this sort of thing and it just gets worse when they're sick. I also find my kids sometimes sleep better with the head of their beds raised, even if they don't have a cold. You can use a slight wedge under his mattress or get short risers for the front of the bed frame at night.