Naruto was always discriminated against by the people of the Leaf Village because he had the Kyuubi inside. However, he is the son of the 4th Hokage and he was the one who sealed it inside him. Why, then, did they discriminate against him if it was in order to save the village?
The details of how Minato sealed the Kyuubi inside Naruto, and the fact that Naruto is Minato's son was kept hidden from the villagers. The villagers believed that Naruto is the reincarnation of the Kyuubi, who killed their beloved Hokage. Having experienced the Kyuubi's attack on Konoha, they were also frightened about going near Naruto. Even the people who knew that the Kyuubi was sealed inside Naruto were worried about their own safety, and wanted to stay away from Naruto.
The Masked Man pretty much nailed it. For future reference, even the fact that Naruto's mom, kushina was giving birth was kept secret, as the seal on kyuubi is weakest during child birth. So, if someone told the villager's that Naruto was the son of Minato and Kushina, when no one knew she was even going to give birth, it could be hard to believe. Especially, when only a few people knew about it. Furthermore, it was probably safer for Naruto if people didn't know that he was the Hokage's kid. That title brings a lot of enemies. Even Konohamaru had people following him 24/7.