I've learned from past experience that the way they treat you at work really impacts your illness. I can't see where the ADA or FMLA or any of the laws would protect you for wearing flip flops, but wearing flat shoes in general should qualify as a reasonable accomodation. If your company has a written policy about management not wearing flip flops, maybe this is his way of pointing that out (albeight a really bad way). Now, if he allows other people of the same level (managers) to wear them but not you, you should be able to file discrimination charges. Can you wear some type of flat dress shoe and be as comfortable as you can in flip flops? I understand not wanting to rock the boat by complaining while you still work there, but if you have enough to take him down or at least get him in big trouble, go ahead and report him. You shouldn't have to put up with that and make yourself sicker over it and other employees shouldn't have to put up with his treatment either. Don't let him get away with it or he will just keep it up.
I've left two jobs due to the way I was being treated and the fact that it was making me sicker (which in turn made them treat me worse...vicious cycle).
Crohn's Disease with Arthritis, Non-Erosive Reflux Disease, Gastritis, Hashimoto's Thyroiditis, Endometriosis, Depression/Anxiety