Jane does care for her cousin St. John, but more like a brother. She considers his proposal of marriage very seriously because it was not uncommon back in the 19th century for a girl to marry a cousin or to marry without romantic feelings. Some marriages, in fact, were done for wealth, social status, or mere survival and without love. But Jane Eyre is not a common English girl. She is an intelligent and passionate woman who knows what she wants and won't settle for anything less. After being tricked by her true love, Mr. Rochester, considering St. John for marriage would be logical and safe for a woman in her circumstances. Jane always dreamed to have a safe and loving family because she didn't grow up with one. St. John could have provided that for her, but deep down she knows that he is emotionally and passionately unavailable for her.
For example, Jane knows that St. John deeply and passionately loves Rosamond, but he turns down a deep, passionate love with her because he values his ministry over living a life for himself. It's as if St. John feels he must suffer throughout life and deny himself joy in order to get to heaven; and this, in fact, is not how Jane feels at all. Jane is a good and pious woman, but she also seeks the best for herself. She knows she would not be happy with St. John down the road or immediately. Jane explains the situation as follows:
"Alas! If I join St. John, I abandon half myself: if I go to India, I go to premature death. And how will the interval between leaving England for India, and India for the grave, be filled? Oh, I know well! That, too, is very clear to my vision. . . He will never love me; but he shall approve me" (411-412).
Later, she tells him she will go as his sister but not as his wife, so she doesn't completely reject him. But she can't bring herself to live a lie. He rejects the sister idea because it would look bad and bring up suspicions among those he teaches and works with. So, it doesn't work out for Jane and St. John to marry.