There could also be rogue ninja who see Naruto as a threat because of the Kyuubi's protection. They might fear that Naruto will grow too powerful and decide to take him out before he becomes a real danger. These rogue ninja could form groups or work alone to try and undermine Naruto's safety.
Often, it could be the Akatsuki. They are always after the power of the tailed beasts, and with Naruto being protected by the Kyuubi, they would be major antagonists. They might come up with new and devious plans to try and get to the Kyuubi within Naruto.
Often, the Akatsuki still remain as main antagonists. Since Naruto's fusion with the Kyuubi makes him more powerful, they would be even more interested in capturing him for his power.
Another potential antagonist could be an inner demon within Naruto that is a manifestation of the Kyuubi's corruption. This inner demon could constantly be battling Naruto's good side, trying to take over completely. And there could be characters who misunderstand Naruto's situation and side with the forces that are trying to 'contain' or 'destroy' Naruto because they believe he is a lost cause due to the Kyuubi's corruption.
One possible group of antagonists could be those in the Hidden Leaf Village who still hold a grudge against the Kyuubi. They might see the daughter as a threat and try to get rid of her. Another could be rival villages that fear the power she might possess and see her as a weapon that could be used against them in the future, so they would try to eliminate her before she becomes too powerful.
It could be Orochimaru. He's always been after power and Naruto's unique abilities would be very appealing to him. So the fem Kyuubi would have to constantly be on guard against Orochimaru's schemes.
The Akatsuki could still be the main antagonists. Even though Naruto has accepted the Kyuubi, they might see his new power as a greater threat or a valuable asset to capture. They could try to take the Kyuubi from Naruto to use for their own evil purposes.
The main antagonists could be the villagers who fear Naruto's mini Kyuubi form and try to drive him out of the village. Their prejudice and fear act as a major obstacle for Naruto, who just wants to be accepted.
The Akatsuki could still be the main antagonists. Even with Naruto's training by the Kyuubi, they would be after the tailed beasts. Their goals of collecting all the tailed beasts would put them in direct conflict with Naruto. And they have some really powerful members like Pain and Itachi.
In some fanfictions, the Kyuubi's protection might lead to Naruto having a special bond with nature. Since the Kyuubi is a powerful force, it could influence Naruto's chakra in a way that makes him more attuned to the natural elements around him. This could give him an edge in battles, like being able to manipulate the environment in ways others can't.
Well, the main antagonists could be a group of rogue ninja who are hired by a powerful nation to take down Naruto. Since he is unkillable, they would have to use more underhanded tactics like trying to isolate him from his friends and allies. Or perhaps there is a dark force that is awakened by Naruto's unkillable state, thinking that he is a threat to the balance of the ninja world. This dark force could then become the main antagonist, trying to destroy Naruto at all costs.
Obviously, Naruto is one of the main characters. His friends like Sasuke, Sakura, Kakashi, and others are also likely to be main characters as they are the ones protecting Naruto.