The main thrust of O'Connor's "Good Country People" deals with the feeling of intellectual superiority.
Joy/Hulga feels she is the only one who truly understands the human condition. Her vast education has made her aware, she believes, that existence is meaningless. She believes in nothing. She's a nihilist.
In other words, she knows better. She knows better than to put trust or faith or meaning in people and traditional values. She "knows better" than the other characters in the story.
In the climactic scene of the story, however, she proves to suffer from the same ideas and notions as the other characters. She trusts the Bible salesman, and is aghast at his true nature, because she, too, thought he was "good country people." (The use of that phrase by O'Connor is, indeed, ironic.) She thus reveals that she, inspite of all her snobbishness, believes as her mother believes.
Manly Pointer (the name, I'm assuming, is not lost on you) also crushes her feelings of superiority when he, ignorant and uneducated as he is, too recognizes that existence is meaningless. Who more than the poor understands the negative side of life?