The dietary laws of Swedenborgian religious doctrine, which John Chapman adhered to, forbade the use of techniques like grafting to improve his apples, so he had to grow them from the seeds; hence, they were useless as food due to the small size and bitter taste, and could only be used for making cider. They could never have been used for making pies as the apple song claims. The cider was actually far more nutritious and safe to drink than the water available in the areas Johnny visited, so by selling the people there his apple seeds, Johnny actually saved hundreds of lives.
This short is based loosely on the life of John Chapman (1774-1845), a clergyman of the New Church ("Swedenborgianism") and fruit cultivator in developing regions of the United States. His agricultural innovations involving apples earned him the moniker Johnny Appleseed.
The cartoon states that Johnny Appleseed became a trusted friend of all animals. While the depiction is obvious hyperbole, the basic sentiment is correct. At some point, John Chapman adapted a fully vegan lifestyle, refusing to harm any animal for any reason. This made him a truly remarkable rarity in a society where the vast majority of the population made their living as fur trappers and/or meat farmers.
At the beginning of the short, a book of American Folklore is seen opening, and three pages mentioning legendary American heroes are shown before John's. They are in order: Paul Bunyan, John Henry, and Davy Crockett. (This scene is edited out in some showings.) Disney would later make films about all three men: the TV miniseries Davy Crockett: King of the Wild Frontier (1955) and its prequel Davy Crockett and the River Pirates (1956), and the short cartoons Paul Bunyan (1958) and John Henry (2000).
In the Little Golden Book adaptation of this cartoon, which was published in 1949 and includes actual illustrations from the Walt Disney Studio, a scene is shown where Johnny rescues a rabbit trapped by a twisted vine in the forest. This scene is not included in the actual cartoon, which suggests that it was a story idea that got replaced by Johnny encountering the curious skunk and petting it.