I would argue that the main idea behind the story is that love conquers all.
Throughout the course of the story, Jane experiences all manner of setbacks, most of which would defeat the hardiest soul. Yet at every turn, she picks herself up, dusts herself off, and moves on, determined to live the kind of life she wants to lead. This is because Jane, despite all the many terrible things that have happened to her, is a strong person. And what gives her strength more than anything else is the power of love.
It's love that gives Jane the strength to defy the rigid conventions of the society in which she lives and to follow her heart. It would be all too easy to subscribe to the prevailing value system and marry someone she doesn't love, like St. John Rivers. But Jane remains true to her heart and waits for the right moment to marry Mr. Rochester, the man she truly loves.
One can't be certain of Charlotte Brontë's precise motives in writing Jane Eyre, but there's a fair chance that it was because she wanted to challenge respectable society's attitude to marriage, which tended to be regarded as a business arrangement—it wasn't called the marriage market for nothing—rather than a heartfelt expression of mutual love.