Because Luke is his son and he still cares about him. He just tries to hide it from the emperor and in the end has to kill him to save Luke.
The problem is the audience only ever finds this out in the final movie so it doesn't make a lot of sense in the first two films. I'm not sure if there was a good way to address this though because the only option would have been to have a scene where Vader basically explains all this to Luke. It seems a bit late in the story for it really to be relevant.