I get exposed to a lot of bugs at work and used to get 4-5 colds a year. Not flus.
Since riding to work I get less than 1 a year now.
I can't tell how many times I've felt a cold coming on and the ride seems to burn it right out.
I tend to dress warm and ride fast though. I think getting my body temp up and blood really moving does wonders.
If I get any symptoms I generally dress warmer and ride slower. Seems to help.
However if it really gets into your lungs don't ride (and stay home).