Ah, such is the ultimate truth that all moms discover when their children have to go to daycare. They always seem to be sick. My best advice is to do two things:
1.) Closely monitor his diet and make sure that he's eating well. His body needs all of the right nutrients for his immune system to function optimally. Also make sure he's drinking plenty of fluids and that he's getting plenty of sleep. Wash his hands when you bring him home too.
2.) Have a talk with the provider. She should have no problem with you asking questions about the sanitary routines she takes the kids through every day. For instance, she should be having them wash their hands several times a day (helping the little ones like your son) and she should be sanitizing all of the toys every night, especially if one of the children is sick. Also ask her about her policy regarding sick children (i.e parents not bringing their sick children in to infect all of the other children) and ask if it can be enforced a little more strictly. Don't feel bad about asking all of this, you are your son's mother and you have every right to inspect and monitor his daily environment for any threats to his health and safety.
That being said, your son's immune system should adjust eventually. It does take a little time, and even then it always seemed with my oldest (who was in daycare a lot while I was in the military) always had at least a runny nose. Just do what you can and comfort him for what you couldn't prevent.