I haven't heard any customer comments about similarities to the Confederate flag before yours, Family Doc. Here is an explanation of the design elements so you can discuss them with curious friends.
Dr. Koop helped design his tie with certain symbolism in mind. The blue stripe with white stars represents his government and military service, and is reproduced from the same pattern shown on his commemorative coin, presented to him by the Navy. (Dr. Koop's stripes do not cross at any point, as they do in the Confederate battle flag.) Red was chosen for the background since Dr. Koop only likes red ties, especially with dress whites. The gold caduceus symbols represent the medical profession. Together, these three elements are intended to be simultaneously patriotic and medical.
Dr. Koop is very pleased with his tie, and I hope you are, as well!