Isn;t it remarkable how much it helps to try to calmly talk things out ? And even as to her not realizing how you felt -- you may have told her before, but that doesn't mean that she recognized and realized it then. I don't think she meant her commend to hurt your feelings --- she was trying, I think, to emphasize that you didn't need to worry so much about your looks, because she valued your personality, and who you are ( which is something that lasts far longer than anyone's looks ). I doubt that she meant to say she never found you attractive, but that she never based the relationship on only that. As Frusty says, many people, especially women, are much more inclined to feel romantic towards a person's depths rather than superficial looks.
Why not consider getting both of you involved in a few sessions of marriage counseling to further sort things out ?