Another issue with the "well they live in the puddles of oxen footprints in the wild" explaination, is that our highly domesticated long finned brightly coloured bettas bear little resemblance to thier wild cousins. They would not last long if we were to return them to the wild (and there would be possible contamination issus, etc as well).
Having said that though, the practice of keeping them in small cups is obviously not the most optimal way of keeping them, but I can understand where the petstore is coming from as well. Since the males fight, you have to seperate them, but by the same token, the store has only so much space. They are also a very popular fish, so a given store wants to have enough a supply on hand to sell each week. The little betta hex's and similar such "tanks" are just inexcusable however since they are meant to be a permanent home...