Everyone are surrounded by germs of some sort it's just part of life. My friend tried to bring her kids up germ free. Wasn't allowed to go outside and play. Constantly bathing them and whatever else she could. Her kids were sick all the time. They didn't get a chance to build up their immune system while babies. After all Mom you're not germ free either. As long as Dad is clean they're should be no problem.
Try not to worry much. Not too much you can do about cold/flu except for what's already been mentioned.
We live on a little farm (read little poop factory), and my husband is a plumber by trade. Between the human waste he wallers in all day and the animal waste I'm flinging all day, you'd think we'd have gotten something nasty by now, but no, nothing. I'm pretty sure somebody has played outside and gotten poop germs in their mouths, too.
What gets us is "back to school" time. Constant running of noses. The four older ones drag the creeping cruds home from school and pass it on to the two littlest ones. The bigs don't seem too bothered, and the littles are less bothered as time goes on, so I guess it's just a matter of time.
Germs happen. Make sure you and dad use proper hygiene such as washing your hands. My 6m old has only been sick once and my husband and I are both in the medical field touching sick people all day. We both make sure we wash our hands at work and at home- it helps more than you think.