Jody's father, Carl, is very much a man's man—tough, resilient, and very masculine. In keeping with the prevailing conventions of the time, he is also emotionally distant from his son. As such, he is unable to forge any kind of real connection with Jody. Moreover, Jody's relationship with his father is complicated by the pressures of work. Carl works just about every hour God sends on his small farm. This does not leave him much time to spend with Jody, let alone bond with him.
Carl is not necessarily a bad man; it is just that his devotion to being the family breadwinner, coupled with his old-school attitude toward parenting, prevent him from displaying much in the way of love and affection toward his son. Carl's world is a harsh world, a world full of struggle and hard work. There is simply no room in such an environment for the kind of empathy and compassion that Jody so desperately needs, especially after the death of his beloved pony, Gabilan. That said, Carl's stoicism and dedication to the material well-being of his family are admirable qualities, and his example is one that Jody would do well to follow.