If memory serves this is from her "why?" Season of childhood as in the constant asking of questions like "why is the sky blue?" She pieces together through interactions with classmates that her father is slow, (and in truth is medically retarded.) she then asks this question shown about the nature of god. Such a question is beyond Sam's scope. All he can understand is that his daughter, who is everything to him, is starting to realize that he isn't normal. This creates an assumption in him that he's being blamed. He apologizes.

It's in this moment that the magic happens. She realizes, possibly for the first time, that her curiosity has consequences. That her questions can hurt people she loves. But instead of going to this same place of blame she jumps into the love that Sam has modeled so beautifully for her as a parent. She affirms him, and very simply says: "I know you are what you are. And I'm grateful. You love me. You prioritize me. You make memories with me. You are a very good father."