We joke that my SS is allergic to February, but if you look at his routine and health, that's not really far off. Things that factor for him:
1. Poor diet. One winter he was on his own and far from home and ate too many carbs and too little fresh food. Even vitamin supplements didn't fill the gap. He does now take a multivitamin and eats better and is less sick. He was still sick this year, but not nearly so bad.
2. Flu shot. I don't always get one, but with SS's history, we encourage him to do so.
3. Getting run down in general. SS would start off the school year at a furious pace and by Christmas his body was rebelling. He needed to say no to a few activities so he wasn't up til 1AM doing HW. Sleep is so important. If you have interruptions to your sleep habits, regroup and get some rest.
4. Other factors, like indoor allergies. We keep the house closed to keep the heat in, but we also keep rolling around in the same germs and allergens all winter. Occasionally try cracking a window and/or getting out to the park where you can breath in new air. Any day the weather is in the high 40s or low 50s, I try to remember to crack a window for a little while. If your family is sensitive to dust, then make sure your ducts are clean.
I also think there may be some validity to allowing them to get minor germs so that when they get the bigger germs, their systems are ready for them. The reason kids get so sick in school at first (and after long breaks) is that the other kids bring in new and more interesting germs to share and those whose immune systems haven't seen those germs before get sick. Same with daycare. Same with a new office. It'll even out. Now, I'm not saying I encourage my DD to eat dirt and never wash her hands, but I also try not to slather her in hand sanitizer, either. We wash hands after blowing noses, cough into our elbows, and make sure that hands are clean before we eat. Good point someone else had about toothbrushes, too.