Personally, I feel like this is the feelings of a father who lost his daughter and is now questioning faith/God. How he says "she was a princess, she could've been a queen" shows that she never had the opportunity to grow up.
Then when singing about the guy, I feel like it could be some careless guy who caused her death, maybe drunk driver? That's how I have always understood this song.
A lot of people question their god when someone who they see as perfect and undeserving of death dies.