This is a really good question, and one that has been asked many times. Why would Jane Eyre end with St. John, instead of with Jane? In chapter 38, Jane is giving us a detailed account of the people we have come to care about in the novel. Of course, she starts off by telling us "she married him", so we know she and Rochester have gotten married, and that her love has healed him.
Throughout the novel, Jane has struggled with people mistreating her in the name of religion. She had to endure horrible conditions with her aunt and cousins, then was abused at the school, all of these people using the name of God as punishment for her. Jane wants her own identity and doesn't want to lose herself again. With Rochester, she has found a love that allows her to be herself. She, in fact, is the one who becomes the stronger of the two. In a twist, Jane becomes a Christlike figure for Rochester.
When her cousin, John, wants to marry her, she sees that she will have to live her life the way he lives it. John wants to go on a mission to India, and expects Jane to follow him. She knows she will lose herself completely if she were to marry John. With the novel ending with St. John, we see what life would have been like for Jane. John is near death, after serving for many years in India, trying to help the natives there. Jane would have had to become the kind of woman she was so afraid of becoming, yet the story ends with John. She reads his letter and knows that he has had a good life, and that his faith has never wavered in all this time.
"I know that a stranger's hand will write to me next, to say that the good and faithful servant has been called at length into the joy of his Lord. And why weep for this? No fear of death will darken St. John's last hour; his mind will be unclouded, his heart will be undaunted, his hope will be sure, his faith steadfast. His own words a a pledge of this- "My Master," he says. "has forewarned me. Daily He announces more distinctly,- Surely I come quickly! And hourly I more eagerly respond, 'Amen; even so come, Lord Jesus."
We see that, although, Jane has struggled so much with religion, and what people do in the name of religion, John is a living example of a person really living his faith. He has no fear of the death that is right around the corner, yet, he longs for it. In his own way, John has found his own happiness and if Jane had been with him, maybe that happiness wouldn't have been there. Jane ends with St. John to show us that, even though, John is alone, his life was full of joy, just as Jane's has been.