This article is from the Living Barefoot FAQ, by Paul J. Lucas with numerous contributions by others.
There are a few reasons:
1. Mind-set. Some store-owners have hangups about bare feet for
absolutely no good reason. Many people are brainwashed into
thinking you _need_ to wear shoes. They just can't handle the
concept of bare feet out on the streets. People tend to dislike
what they don't understand.
Note that mind-set varies with locale: In the Chicago area, for
example, many large chain stores and supermarkets forbid bare
feet. If you go to warmer climates like California or Florida,
barefooted people are much more common so nobody thinks anything
of it. Also, if store-owners chased out barefooted customers,
they'd be doing that all day long.
On a more global scale, countries like Australia and New Zealand
are _very_ barefoot friendly. Many, many people go barefoot
regularly everywhere. Nobody cares and they think it's completely
natural (which it is).
2. Alleged health laws. I have written to my township and my county
and state health departments. There are _no_ laws stating that
customers may not be barefoot in _any_ kind of store _including_
food-service establishments. I know others in other states who
have done the same research: nothing.
I know a guy who complained to the health department in CA about
McDonalds displaying the sign, "No Bare Feet by Order of the
Department of Health." It turned out that McDonald's removed the
signs (in CA) and wrote a letter of apology to guy who complained!
For an exercise, I called the headquarters of a large supermarket
chain in the Chicago area. The woman on the phone was just as
ignorant: she thought it was illegal to go barefoot into stores. I
asked her to give me the statute number (knowing full well that
she couldn't because it doesn't exist). She said she'd have to
call me back. She actually did and told me that there is no law,
but it's their "store policy."
Of course, the bottom line is that a store-owner can refuse to
serve you for any reason so long as it isn't sex, race, religion,
veteran status, sexual orientation, etc, etc. Bare feet,
unfortunately, are not "covered" by anti-discrimination laws. But
you can spend your dollars elsewhere.
As an aside, what does _health_ have to do with it? Do they sell
food off the floor? Yes, when I go barefoot, the soles of my feet
get very dirty...so what? Are shoe-soles any cleaner? Dirt is
dirt. At least I wash myself daily which is most likely more than
people wash the soles of their shoes.
3. Broken glass. Store-owners are so afraid that you will step on
broken glass and sue them, that they just forbid bare feet
altogether. In one respect, this is a ridiculous thing to say. For
avid barefooters, broken glass is not too much of a problem. The
soles of my feet are _very_ thick and tough, the way they are
naturally supposed to be. I rarely injure myself with broken
glass. The store-owners, however, don't realize this.
In another respect, I do have some sympathy for them. The USA is,
by far, the most "sue-happy" country in the world. And the worst
part is that dumb-ass juries enable people to win! There was a
case where one neighbor borrowed another's lawnmower. The guy
decided that his hedges needed a trim, so he picks up the
lawnmower while it's still running and, needless to say, injures
himself very badly. He sued not only the lawnmower manufacturer,
but also his neighbor for failing to warn him that picking up a
running lawnmower was dangerous. He won! Given such verdicts, the
store-owners are just protecting themselves.
Even if I were to cut myself, I would not sue. I am a big boy and
realize the possible consequences of my actions and realize that
most things that happen to me are _my_ fault.