The article at Mother Jones is titled Why Your Supermarket Only Sells 5 Kinds of Apples, but it barely touches on that question (the answer seems to be "because agribusiness"). It's really about John Bunker and his quest to cultivate heritage apple varieties before they are lost forever. See, apples are hard to breed. If you want more apples like the ones on a certain tree, you need to clone it by grafting.
Even when abandoned, an apple tree can live more than 200 years, and, like the Giving Tree in Shel Silverstein's book, it will wait patiently for the boy to return. There is a bent old Black Oxford tree in Hallowell, Maine, that is approximately two centuries old and still gives a crop of midnight-purple apples each fall. In places like northern New England, the Appalachian Mountains, and Johnny Appleseed's beloved Ohio River Valley—agricultural byways that have escaped the bulldozer—these centenarians hang on, flickering on the edge of existence, their identity often a mystery to the present homeowners. And John Bunker is determined to save as many as he can before they, and he, are gone.
Bunker is an apple detective, who looks for such old fruit-bearing trees in order to preserve their genes by grafting. Read about his work, and the history of apple cultivation in America. Link -via Boing Boing