He blamed John for the death of Mary and John's twin. The truth is that Thomas attempted to abort both of his children which is what killed Mary and John's twin, but John survived. John and his father never got along, which is what led to John running away.
Thomas was killed by the Family Man, but when John was a child he had cursed his father to a slow death, which resulted in his father remaining in the world as a ghost. When John realized this was happening he broke the spell. This sent Thomas to hell (though this was unintentional on John's part).