http://www.straightdope.com/classics/a4_104.html
I had read that the reason winter tends to be the cold and flu season was not because of the cold, but because a lot of people tend to stay inside more. We don’t like to be out in the cold, so we all stick around indoors where it’s warmer - for us and the germs. So we end up getting more exposure to germs, as well as probably creating more germs since a lot more of our activities are done inside (not to mention that those unhygienic people we all know are sharing our space indoors and touching things more frequently as well).
So even though the cold weather does make it harder for germs to survive outside, we provide a cozy environment for them to thrive in with us.
–Sarah 