B.A.
I highly recommend that you read the book "How To Raise a Healthy Child in Spite of Your Doctor" by Dr. Mendelsohn. He's very reassuring and, as a pediatrician, he believes that mothers know much more about their children than any doctor could.
That said, I have never tried to say "no" directly to a doctor... though I have taken a prescription and not filled it before. I usually smile and nod and say "okay" and if I don't feel that myself or my child need the medication I simply don't get it. Parents do have the right to have the final say. However, some doctors can sometimes get very defensive and even nasty when they are questioned.
This is one of the reasons my family doesn't go see a doctor at all between regular check-ups. If I were you, I would discuss this doctor's behavior with your son's regular doctor. His attitude and actions were totally uncalled for.
As far as your son's flat feet go - my husband had completely flat feet. He started going barefoot everywhere and now he has low arches. It's something you might want to look into since it's totally free and risk-free as well :)
http://www.barefooters.org/faq/09.html
Best wishes!
~B.