The main arguemnet for eating food off the floor is to not be wasteful. It's not that your screwing your immune system by not eating off the floor, it's just one of the many habits people have to avoid all germs. But You aren't increasing your risk of getting sick by any significant amount either.

The breathing example makes no sense either because if I breath air where I live and am at 99%, then I would have a 100% chance of being sick if I went on vacation to China. My neighbors just got back from there a few weeks ago and did not get sick.