In the Air Force, it's because regulations state so; and only when deemed to affect your duties. Basic issue combat boots weren't exactly accomodating for miles of marching. People with foot problems just had a rougher time with the basic combat boot. Now, at least in the Air Force, they've lightened up on the type of boots you can wear, and so many people where black high top like athletic shoes for comfort, even if they aren't going to be marching.
Air Force Instruction 48-123:
"Pes planus, symptomatic, more than moderate with pronation on weight bearing which prevents the wearing of a military shoe, or when associated with trophic changes."