I think the song is special because it's the only Dylan song that came close to actually being a folk song at a time when Dylan was being hailed as a great folk singer . Like other Dylan songs it has taken on layers of meaning that perhaps weren't apparent to the composer himself in the ten minutes it took him to write it.
Dylan was a rebel - an individualist never comfortable as the voice of his generation . One reading of "the answer my friend is blowin'in the wind" could be that Dylan was articulating his own cynical answer to the unanswerable questions he posed. Blowin'in the wind is the best course for the individual to take ,just take things as they come.