This song doesn't have to be thought of as a reference to god or religion. A song can speak its message to anybody regardless of belief, and the message doesn't have to be the same for everybody. I'm atheist, and not afraid to admit it, but this song still resonates deeply with me and carries a powerful message, a story.
The first time I listened to this song, it touched my heart. This song has a deep meaning behind it. To me, this is the story of having so much happen in your life, everything is falling apart, and you need someone to help you up. Then you find someone, they call out to you. You find someone who gives you the help, the comfort, healing and love you've so desperately sought for so long.