I hear you. Sometimes, the success of small businesses are exquisitely sensitive to public perception. "Don't go to that store, because they let [person(s)] in there."
Do all the chain stores in your area allow people to go barefoot? If not, that might be a good place to start. Once people start going barefoot regularly in those, then maybe the sign in the local store will come down on its own.
Also, frequently the chain stores would offer more exposure for barefooting. Not going to the local store until they permitted barefooting, would be neglectible on their business (at least until barefooting becomes more common).
The chain stores mostly seem OK, but I'm not militant about it. When I'm out and about doing errands, I usually bring sandals along, although when I haven't, there's never been a problem. Most of the chain store shopping is done by my wife anyway.
The problem with the local place is just that, it's local, very convenient for picking up a few things on the way home, and like I said, they have a great butcher. So it would be a real hassle to drive out to the suburban shopping area, or to St. Paul's Midway area, just to pick up a few odds and ends on the way home from picking up the kids, or on a weekend outing.
As for other customers, I doubt they care. This is a neighborhood full of college professors and professionals, who probably like to imagine themselves as tolerant, liberal, NPR-type folk. They all gush when I bring in my beautiful biracial children.
So it's really just the peevishness of the owners and their sons/nephews, who are overweight and unhealthy-looking. Still, they're nice, calm people (except for one duffus who seems to have 'issues' that extend well beyond phoot-phobia). So perhaps with the help of the SBL's "A Case for Bare Feet" pamphlet, which I've just printed out, they will be open to the voice of reason and overcome their silly, but quite common, prejudices.
Nobody at the local school or our daycare seems to care, and those are the places where I most frequently enter barefoot. And my kids usually kick off their shoes as soon as I arrive, so I don't think I'm making them feel uncomfortable for having a slightly non-conformist dad. Most of the parents are pretty normal-looking, although there's a few loaded with tats, piercings, and stuff like that, and several other biracial families. It's a pretty live-and-let-live neighborhood overall, although of course they are seldom confronted with practices that really run contrary to their notions of normal.
One thought if I lose this battle, is to come in with a helmet and work-gloves every time I shop at the store, since it's so dangerous. Would be a nice humorous form of protest.