Jonathan was simply trying to protect his son from being discovered and hounded the rest of his live by the government and military. He still made it clear that he expected Clark to do great things in the future, but just didn't think he was quite ready yet to reveal himself to the world.
Generally, when parents tell their children one thing through their words but demonstrate a completely contradictory thing through their actions, it's going to be their actions that the children grow up emulating.
Jonathan demonstrated self sacrifice to Clark in a way that would stay with him for the rest of his life. I don't like the way they did it, but I get the message.
But back to Superman Returns