The ending, in which Jane and Rochester marry, is happy, if bittersweet.
It is bittersweet because Rochester has been disabled by the Thornfield fire, losing a hand and his eyesight. He is no longer the intimidating Byronic hero. Jane, too, has been through a series of sobering experiences.
It is, however, these maturing experiences that make it possible for Jane and Rochester to have a happy marriage. They marry on the basis of an honest foundation, for Bertha is dead. Rochester is disabled, but his disabilities allow the two to have a companionate marriage based on mutual equality. If Jane, the poor, quiet, dependent former governess had married Rochester when he was "whole," it would have been an unequal relationship, with Rochester in control. Now, Rochester is as dependent (or more) on Jane as she is on him.
They do have a happy marriage, filled with a deeper, sadder, more mature happiness than that perhaps experienced by frivolous young people in the first stages of passion. They appreciate each other all the more because they both have suffered. They have both known what it is like to feel lonely and despairing.
Brontë seems to be commenting on patriarchy in implying that a man needs to be disabled in some way for an equal marriage to take place.