In each of the three stories; Jack and the Bean Stalk, Gilgamesh, and the Odyssey, there is an encounter by a human with a savage. In Homer's, The Odyssey - Book IX, "Cyclops", Odysseus and his men plot to kill Cyclops. In Jack and the Bean Stalk, Jack prides himself into the home of the giant. In Gilgamesh, Gilgamesh finds himself his equal match, who happens to be a wild man.
While we ourselves can most often relate more to the human than we can the savage, it does not mean our sympathy will necessarily be geared towards them. Odysseus and his men were frightened by Cyclops' actions and his loud voice, while none of them felt any remorse for the thievery they had partaken in. Being that Jack is so poor, he too finds it fair for him to steal from a giant. Gilgamesh, being the all-mighty of the land sees no wrong in stealing all the virgins.
While the men in these stories are fearful of their savage opponents, they feel threatened only because they are unfamiliar with their ways. While the men thought the three antagonists to be uncivilized it was only because they were judging them based on the qualifications and standards of their own society. While the three savages most certainly do not fit into those standards, it can also be said that the three men would not fit into their standards either.