Airway hyper-reactivity is a fairly common problem in young children. In some of these children it simply goes away over time. In others, it becomes asthma. The most common association for those children who develop asthma is their family history of allergy or asthma.
As far as "natural medications", these usually do not hurt a child and may provide relief for a few. However, they should not be a substitute for the Pulmicort Respules™ (budesonide inhalation suspension) and Xopenex® Inhalation Solution (levalbuterol). If your child has wheezing and coughing these two medications are excellent medications to control these symptoms.
If you continue to have concerns, you may ask your pediatrician to see a specialist who deals with children who have similar problems as your child. These are usually pediatric pulmonologists or pediatric allergists.