I too have wondered why I have heard that same comment over and over again, "Oh, I can't wear heels." Or, alternatively, "I can't wear heels anymore." I understand that there are some valid physical reasons why somebody can't wear heels, or at least not for very long. However, thinking back to my own experience, I think a lot of these obstacles can be overcome. It's just that overcoming the physical challenge of wearing heels requires a lot of work, and I don't think most women want to put in that kind of effort. Or perhaps it would never occur to them that it's a skill rather than just a fashion choice.
In any case, it's generally a conversation that can't go well. This is why I tend to say very little in reply to such comments, and do much as you did, saying something like, "Ehhh, they're really not all that bad."