I'm sorry to read that your little one (and you) are dealing with this. It stinks so bad when our kids are sick!
I'm a FT working mom and both of my sons are in daycare and have been since 8 weeks. My 1st son was sick ALL the time at the first center we were at and we moved him to a different center. He still got sick, but not nearly as often. So, yes, some centers can be A (not "the) cause of your child getting sick more often.
At the same time, we have him and our 12 week old in a center now and the 12 week old hasn't ever been sick (knock on wood). The center we go to IS very clean and they DO sanitize, wash their hands, etc often. I've come at all different times to pick up my sons with no notice to them and I've yet to find something that bothered me or a red flag with regard to cleanliness.
I can understand your frustration and probably some guilt, too. Heck, I still have guilt and I'm very happy with our center and have been using daycare for over 2 years. If your son hasn't been exposed to a lot of germs being home with you, then this was bound to happen. Unfortunately, this time of the year isn't the best, either.
I'd take your concerns to the center director - in a non-confrontational manner. Ask her what the sick policy is and how strictly they adhere to it. I'm sure as a new daycare Mom, she will be understanding. Sometimes, the problem isn't as much the CENTER as it is irresponsible parents who load their kids with Tylenol in the AM to hide a fever or cold and drop them off at daycare. Symptoms are hidden and by the time the Tylenol wears off and the parents are called, germs have been spread. It's frustrating. But, "bad" parents are going to be something we all deal with as time goes on. You know?
But, I have to say to those "anti-daycare" posters...Our group of friends is split about 50/50 with daycare and SAHM's. And, the SAHM kids are sick just as often as the center kids. My closest friend has had her son to the ER more than once for severe colds/croup/dehydration and he hasn't spent a night away from his mom yet. Kids are kids and they get sick. If it wasn't now at daycare, it would be in pre-school or kindergarden.
So, don't be too hard on it yet. I'd take a look around at the center when you are there, stop in at different times and see what goes on. Talk to the director and at this point, if you haven't already, a call to the peditrician may be a good idea.