She made sure the ship ran, and he made sure she stayed alive and ate well. While she knew about her responsibility to keep the ship going, she didn’t know about the commitment he secretly kept in regard to her: he would protect her, not only physically, but also from the dark things in the world, the dark ideas that can plague a man’s mind, turning him into a husked-out shell of himself. That innocence and happy abandon she brought to the ship and shared willingly with the rest of the crew would be kept intact as long as he could help it. He didn’t want Little Kaylee to turn into a cynical cold person,knowing nothing but pain and mistrust, unable to respond to love, and affection, and above all else, unable to find happiness. That’s why he let his natural affection for her shine. Besides, who couldn’t be affectionate towards her? Hell; even Jayne, one of the most calculating of mercs in any 'verse, made an effort to be good to her. And he never insulted her directly or purposely, especially after the dinner incident. The Captain never wanted her to look at someone as a mere means to an end, but rather as a person, capable of altruism and love; he didn’t want her to take on any of the characteristics he saw in himself, kept buried beneath the surface, characteristics that fought with the ideas the innocent little boy inside him still, through some miracle, held on to. Never, as long as he breathed, would Kaylee witness up close and personal those ugly aspects of human nature. She was his personal responsibility, his light, his hope for a brighter future.