First, a quick note on how Hermione described Harry. The way Hermione understands Harry—that he doesn’t really have friends, only tools—is how Harry understands himself. But that’s not the way Luna understands Harry, and the way Luna understands him is the way I understand him. Harry does genuinely love his "tools"; that is the "fondness" Hermione speaks of. Hermione and the others really are his friends. He also genuinely feels compassion for people who are being hurt; it’s why he steps in when he sees bullying. But he struggles to process these feelings without rationalizing them through the lens of his three rules. It’s not clear if he will ever free himself from these constraints. (Though perhaps the certainty and permanence of his tie to Hermione would help him to let her in more.)