The barn loft is small, cramped, confining, and dark. It's the home of Doodle's baby sized coffin. The cramped loft probably comments on or reflects the minds of the characters inside it. If a character is trapped in a tiny space, he likely feels trapped for other reasons too.
It's interesting to note that eight-year-old Brother shows Doodle the coffin before he teaches Doodle to walk. He loves Doodle and is developing a sweet relationship with him, but he's still trapped by Doodle. Doodle still isn't quite the brother he has in mind. He needs special care and has to be carried around. Brother is caught between loving Doodle, and wishing he didn't have to deal with him, and be embarrassed by him.
These feelings are normal, but Brother doesn't have anyone he can talk to about it. It doesn't sound like something he could bring up to Mama or Daddy. So, Brother expresses his feelings to Doodle by taking him to the barn loft trapping him in it. He wants to show Doodle how it feels to be trapped or scared. He does it, as he admits, in a mean way, that isn't productive or healthy for either of them. Still, is it that big a deal? If Doodle had lived it wouldn't be, but since he didn't, it is. A piece of Brother will always remain trapped in the barn loft, being mean to Doodle.