D.,
You have two options. 1. Tell people not to touch your child. But understand, that sends the wrong message to the people and the wrong message to your child, no matter how polite and firm you try to be. The people will think you are rude and/or paranoid, and you are teaching your child to be afraid of human contact.
Think about this: If you are pushing the cart in Target or the grocery store, have you wiped down the handle with antibacterial wipes? If not, your hands are just as germy as the person who reaches out to touch your child.
I think you are over reacting, because anything you or your child touches when you are outside of your own home has trace amounts of fecal matter, urine, snot, blood, semen, and a whole host of bacteria on it from people touching it who have not washed their hands.
If you are concerned about germs now, you're going to go nuts when your son goes to school. He will be sick more often than he's not. How many preschool or elementary school kids wash their hands regularly in a day after sneezing on everything, picking their noses, scratching their butts?
Choice 2. If after realizing how many germs he's exposed to every time he leaves the house you are still feeling uncomfortable about the germy people who "might" touch your son, then just clean him up after someone touches him.
Keep a packet of wipes in your purse (for use on faces) and a little bottle of hand sanitizer for hands--especially before his little hands take that snack from the ziploc bag into his mouth after he's been hanging onto the grocery cart handle. Wash your own hands well and often and teach your child to do the same, including teaching him not to touch his own face after handling things that are not clean.
I'm not a germaphobe, but I am rarely sick (same with my son) because I clean my hands frequently throughout the day when I run errands and I keep my hands away from my face (a major "entry point" for many germs). My son now keeps a small bottle of hand sanitizer in his gym bag, backpack, and his car.
It's no big crazy deal; we're not running around wrapped in saran wrap and wearing surgical masks, we've just made personal hygiene part of everyday life, and we are healthier for it.
Don't worry about it so much. Do what you can do, and don't sweat the rest.
Good luck.