I think people are afraid of
I think people are afraid of what they don't know. My guess is for the general population people with bare feet (except for the beach in summer, go in the same category as people who are homeless/poor, people who are mentally ill, people who are too lazy to work and people who don't "fit in" for some reason.
I think "Born to Run" has helped a lot and prejudice will go down over time. In the meantime I like the approach of a response that is proportional to the offense. If someone is curious and just clumsy in how they talk give em a break and explain. I like to mention to people that in some sports people are routinely barefoot (martial arts, ballet, gymnastics).
If someone is offensive ignoring is my first choice, if that does not work I like to ask the person to explain EXACTLY HOW they feel about this. Given that most people like to be heard this might diffuse the situation enough to where they realize that they are dealing with an intelligent human being in spite of the bare feet and it might open a door.