The problem was, Ben didn't think this was all a case of misunderstandings. Those could be fixed by people telling things they'd agreed they wouldn't and everyone talking it out, and no one was doing that at all. "Maybe there's a reason there's not, maybe there were people and demons before like them and they turned out bad anyhow."
Despite the maturity of his language or subject matter at times, despite the level of maturity he could show in serious situations when it warranted it, there were many concepts that could elude this nine year old who was, in the end, still just a kid. Kids weren't meant to have a greater understanding of the meaning of life or the world yet, to see things in infinite shades between black and white. In a child's world, things could be narrowed to their simplest forms. Friends and enemies. Likes and dislikes. Loves and hates. Good and bad.
In Ben's world, if Ruby wasn't different, meaning she was good, then she was just the same as any other demon, meaning she was bad like all the rest. If she wasn't fully helping his uncle, she was completely hurting him. But how did he voice that concern and his reasoning to Castiel, someone who was loyal enough to Ruby that Ben still believed he wouldn't really see what Ruby was doing to him?