To me, this song seems to be either about two things.
1. His previous love left him and the rain reminds him of her. He cannot stand being away from her, and the fact it's raining outside causes him to just let his feelings escape for her. When he lets it go, he feels baptized anew - meaning he is relieved from the pain inside. He was lovesick, now he's ok.
2. His previous love died and the rain reminds him of her. He is doing his very best to cope with the circumstances, but when it rains, he breaks down. He says it "feels like it's rainin' you" because it's the closest he'll ever be able to get to her until he meets her in Heaven. When the sky opens up, they're closer. The rain represents her touch, smell, love. He wants it to always rain so he can be closer to her. When he is standing in the rain, it baptizes him; it makes him feel better about continuing in life. He feels free, like baptism is suppose to feel.
What does anyone else think?