We don't digest food exclusively with bacteria. They play a role, of course, but our digestion is done through things with hydrochloric acid and various enzymes produced by the stomach. The bacteria in our stomach is pretty much strains that can both survive the acidic environment and can consume things we cannot digest at all. Various fibers, for example. They help as they consume it and shit out stuff we can digest. Often the things they consume that are indigestible to us are the result of our own breakdown of other compounds; making the process symbiotic.

Also, the environment on a kitchen counter is wildly different than the environment inside out stomach, so airborne bacteria- even if we were to presume these were the exact same kinds of bacteria present in our stomach - being uninterested in foods in the open air doesn't really translate to the idea that the food is indigestible. Many gut bacteria rely on us to break down foods into the things that they can digest, so a colony couldn't start on the surface of the same food(s) in the open air.