Hi J.,
Unfortunately, I think you're just dealing with the automatic problems of daycare--- and other than quitting work to stay home with your son, there really isn't much you can do about it, unless you put him with a private sitter- your mother, a good friend, etc.
Every single study on the subject has shown that children in daycare get sick far more often than those who aren't in daycare. And it's only natural that that would be the case.
Obviously, most parents don't have jobs that allow them to stay home every single time a child gets a runny nose/cough/cold, etc. But that runny nose will end up in 75% of the other kids at the daycare. Cold germs spread SO quickly-and even if the daycare is 100% on the ball with disinfection, handwashing, etc (which NEVER happens) there's nothing they can do about germs flying through the air with every cough and sneeze.
That's probably a huge factor in the number of ear infections your son has had. Another factor is the "bottle in the crib" thing. Daycares are notorious for laying a baby in their crib with their bottle. They shouldn't do it-- (MAJOR contributor to ear infections-- laying down to drink-- the nose, mouth and ears/eustachian tubes are all connected) but honestly, what else can they do if there are 4 or 5 babies crying at the same time? Or what if they're trying to get them all to take a nap? They can't hold all of them... So, they put them in a crib and give them a bottle.
Rotovirus comes from fecal matter getting into the mouth, and AGAIN in most common in children that go to daycare. That could be from a worker not washing their hands enough after changing 30 or so diapers a day, then preparing food and feeding the children. It could also be from children sticking their hands in their diapers, then playing with toys which your son then sticks in his mouth.
Proper handwashing and disinfecting toys can help with this, but again reality sets in. You're going to be hard pressed to find a daycare that washes all their toys EVERYDAY. Most do it every couple weeks or so (if you're lucky).
The truth is, the more kids, the more illness-- that's why daycare environments have the highest rates of illness. As kids get older, and they become less drool-y, less "hand to mouth" with their own hands, toys-- everything they pick up-- they generally get sick less and less.
If it really bothers you-- and if there's anyway possible, maybe you can sit down with your hubby and figure out if it's really necessary for you to work and/or if you can work different hours. (Or if you're going to school, maybe you can take evening classes and your son would be home with daddy. )
I worked in daycare for years... and frequent illness is just a part of the territory. Other than not sending them, there really isn't too much that can be done to prevent it.
Best wishes!
T.