Lyric discussion by Me2 

the song is about Dave questioning faith through prayer, free will and the requests of mankind towards our needs and fate that has already been written.

if the girl became sick and died. it was their fate. no amount of prayer would have changed the event. the expectations of mankind towards God can become skewed as we look through our eyes the activities of God within our daily struggles instead of through Gods eyes and the reason for the event occuring.

dave is learning the knowledge of Good and evil. as he is experiencing things he didnt expect.

he's learning how to be a humbled creature

Firstly, I view Dave as using the word "cancer" broadly to mean an evil condition or something that spreads destructively, NOT only the medical disease.

I Agree with Me2's interpretation. I feel that this song is about the man's struggle with faith--specifically reconciling the evils of our world with an omnipotent creator who has the ability to cure them.

Additionally, the last verse :

"Oh, you may find you're faithful You may find out the reaction"

I thought Stefan's daughter died of SIDS, not cancer.

An error occured.