This song is so beautiful. I think it's about a man who showed a special & unique woman that he likes her. Somehow she knows he is into her but life brought some circumstance (maybe he met another woman who was more confident than the special one he still likes - and chose the common one, only to regret it).
He compares her to a manger because she's pure and of loyal character so he knows he'll have peace of mind with her. But she's hesitant, not because she doesn't like him, but because she's not the kind of woman who falls easily in love, that's why she's so rare. "Where love has eyes and is not blind" - the end explains a lot. That's why the woman he truly loves is pure and unique, because she doesn't fall blindly for any man but sees well. It's clear that she is sacred in his eyes that's why he doesn't want to change her. His dream is that he'll be assured she wants him and one day will be hers.
Perfect song.