Okay, so Billy doesn't exactly seem to be a church-going boy, but he sure is full of prayers. Over and over, Billy asks God for help when things get rough. In fact, God might as well be a member of Billy's family for all the book time He gets—and he's definitely more important than Billy's sisters. Billy doesn't attend church, but he is certainly a very religious character. So it's shocking—and the real crisis of the book—when he loses his faith (briefly) after his dogs die. You might even say that the most important story Where the Red Fern Grows tells is about Billy learning to believe in God again.
In telling this story, the adult Billy suggests that Old Dan and Little Ann were sent by God in answer to Billy and Billy's mom's prayers.
The adult Billy doesn't actually believe that God sent Old Dan and Little Ann, but they're still a deeply religious force in his life.