The allegory of planting apple trees is one of community and settlement. As Americans migrated west, Johnny Appleseed (John Chapman) was there to meet them with saplings available for purchase. He traveled west and made sure he planted plenty of fruit trees for the migration of settlers. As the apples trees were planted by the new settlers, they grew and provided food and fruit fro making cider (the primary drink of American settlers).
As well, apples that grow in the wild are unique unless they are grafted. Every time a new wild apple tree grows from a seed, it is a wholly new variety. This is an allegorical reference to the mixing of different families and ethnicities in the early days of the United States. As people of varying ethnic heritage married and had children, these combinations of Italian-Irish, German-Dutch and French-Canadian, etc. made for wholly unique types of people who combined the traits of both parents, just as new wild apples represent the qualities of both "parents."
This is discussed in fascinating detail in Michael Pollan's book The Botany of Desire.