It could be Kami, but there might also be other forces at work. Maybe Kami is being influenced by some other dark entity. So while Kami is the one directly betraying Naruto, there could be a deeper, more hidden antagonist pulling the strings. However, based on just the title, Kami is the most likely main antagonist.
Obviously, Kami would be the main antagonist. Since the title says 'naruto betrayed by kami', Kami is the one doing the betraying, which makes him the bad guy in this fanfiction.
Well, Kami is the prime candidate for the main antagonist as per the title. But it's possible that in the fanfiction, the author might introduce some sort of corrupted version of Kami or a false Kami who is the real source of the betrayal. This could add an interesting twist to the story, but still, Kami or something related to Kami is expected to be the main antagonist.
It could be a powerful priest or someone who represents the traditional view of kami. They might see Naruto's forsaking of kami as a threat to their power and beliefs, and thus oppose him.
Maybe a rogue ninja who has somehow tapped into dark powers related to Kami's domain. This ninja wants to use these powers to take over the ninja world, and Naruto, with Kami's help, has to stop him. In this fanfiction, the rogue ninja could have some personal vendetta against Kami as well, which adds more depth to the story.
Maybe a rogue ninja who has made a pact with a dark force. This ninja could see Naruto as a threat to his plans of ruling the ninja world, especially with his new status as a dragon warrior of the kami. He would try to stop Naruto at all costs and might have some dark powers of his own.
In the 'naruto betrayed by kami fanfiction', it could be that Kami has been secretly manipulating events all along. And when Naruto gets too close to uncovering the truth about certain things in the ninja world, Kami decides to betray him. This could lead to Naruto having to fight not only his normal enemies but also this powerful Kami - figure, which would make for a very interesting and challenging plot.
It could be one of the harem members who has a hidden dark side. Maybe she's jealous of Naruto's closeness to others in the harem and decides to turn the rest against him, so she becomes the main antagonist.
Another possibility is that there is a false god or a demon that has influenced the true gods to betray Naruto. This false entity could be the real mastermind behind the whole situation. It wants to use Naruto's downfall to gain more power or to bring chaos to the ninja world. So Naruto not only has to deal with the betrayed by the gods part but also has to uncover the true source of this conspiracy which is this false god or demon.
Another possibility is that there is no single main antagonist. It could be a combination of misunderstandings, village politics, and personal issues within Kurenai herself that lead to her betraying Naruto. For instance, the village elders might be pressuring Kurenai to keep Naruto in check, and at the same time, Kurenai has her own doubts about Naruto's power which could be misconstrued as a reason to betray him.
It might be a rogue ninja from the Wave. They could have a vendetta against Konoha and see Naruto as an easy target to frame and cause chaos between the two places.
It could be a new character, someone who is jealous of Naruto's growing power and popularity among the girls. This person might spread false information to turn everyone against Naruto. Maybe a rogue ninja who has infiltrated the village and has a vendetta against Naruto for some unknown reason.
The Jedi Council themselves could be the main antagonists. Since they are the ones betraying Naruto, they would be the ones he has to oppose. Their actions of betrayal would drive the conflict in the story.