IF YOU AREN'T ALREADY, IT IS TIME TO GET ALL OF YOU ON A DAILY VITAMIN.
AND, don't be a germaphobe. The more kids are exposed to germs, the more their immune system builds up its defenses. I'm not saying let him be filthy. But, don't use antibacterial everything. Researchers are finding that too much antibacterial is just as harmful as never washing. We all grew up using regular soap to wash ourselves and turned out just fine.
AND, don't let children use antibacterial cleanser that you squirt and rub in. That stuff is mainly rubbing alcohol which is poisonous if ingested. If a child puts it on their hands and then their hands go in their mouth before it is completely dry, it can poison them.
The more often you son is in daycare and around other children, the more "immune" he will become. Passing sicknesses around is going to happen whether in day care or at school when he is older. It wouldn't hurt to check with the day care about their cleaning habits, too. Maybe they have slacked a little.
I have been very lucky with my 6yo, knock on wood. He's a 1st grader now, but started day care when he was 7 weeks old. His first year we went through several bouts of ear infections. But, otherwise have been very lucky. He usually goes to the doctor for his yearly check-up and then one other time during the year, typically for the sniffles.
When he was a baby, UTMB in Galveston was doing a study on a Roto virus vaccine. I let him participate. We found out after the study, he got the vaccine, not the placebo. Consequently, we have not had to deal with many viruses at all, maybe once a year. His worst one was at 18months. We had diarreah (sp?) horribly. Literally everything he drank/ate went straight through him for a day and a half. But, I found out when he went back that a few of the kids had had 2 rounds of it. The ones that got it first, got well, then got it again as the others contracted it! I was thankful that we did not have to deal with that.
Good luck and just bear with it, it will get better.