Recently I purchased a pair of minimalist shoes (see photo above) for working in my garden, since my older pair of slip on garden clogs (see photo below) were hurting my feet. My new moccasins have a very flexible sole that essentially protects my feet from nails and rough terrain while allowing a variety of articulations that weren't available with a rigid sole. (Also, if your shoe or flip-flop isn't attached to your foot, your toes will curl in to attempt to hold onto your shoe....which could result in bunions over time.)
Of course, the caveat is now when I wear my old shoes with a rigid sole, I can feel the way my ankles are forced to receive the brunt of impact while I am walking. Your feet really do need a diversity of movements with each step, and that does not happen when they are constrained all the time by our footwear choices.
The 26 bones and 33 joints in the foot really do work well to receive and distribute the impact of the ground with each step. When our shoes have a rigid sole (which now feels like someone strapped a block of wood to each of my feet) then the outcome is your ankle works structurally in a way that potentially may hurt it due to the fact that your foot's natural movements have been removed from the equation.
If your feet cannot articulate properly then your ankles will receive more force with each step which may cause undue and unnatural stress. Overuse syndromes do not need to be the norm if we consider and practice more the natural movements of the body.
Think of all the movements that your hand can perform. Now imagine you have strapped your hand to a block of wood. You have limited the movement in your hand, which then translates to loss of muscle over time. Since your body economizes energy efficiently, it will decide that those muscles in your hand (and, in reality, your foot in constraining footwear) aren't as important since they aren't being used.
Shoe choices DO matter!
Photos from Google