Not going to lie, I shed a tear or two. One of the best fanfics out there in my opinion. I was kinda skeptical at first being that the main character is a human. But it's actually really great!
Did you not read the entire thing? A great father-daughter bond is developed later on, and it especially shows during the end. And honestly, if you found a cartoon character in a box, wouldn't you react the same? After all, it was a young, non-speaking pony that acted like any ANIMAL would, therefor the main character's actions are justified. You clearly didn't read the whole thing or read the rest of it with the mindset of he treated her like a prized possession and were too stubborn to get off of that. He tried his best to protect her by not telling her the truth because he knew it would hurt her, just like a parent doesn't tell their child that the world is actually a place where you grow up having to work your ass off to survive. The story represents bonding moments i.e. failing at baking but still having fun. I'm sorry, but I think if you read the whole thing, you failed to see the connection everyone is raving about, and I don't see how you could.