It could also be that the gods have servants or minions in the ninja world. These could be some powerful ninja who have been corrupted by the gods' influence. They act as the hands of the gods in betraying Naruto, doing things like spreading false rumors or setting him up in dangerous situations.
Obviously, the gods themselves would be the main antagonists. They have the power to manipulate Naruto's world and his fate. They could be some sort of ancient deities who have been watching over the ninja world from afar and now feel the need to interfere.
Another possibility is that there are other forces that are in league with the gods. Maybe some dark clans or organizations that see an opportunity to get rid of Naruto with the gods' help. They work together with the gods to make Naruto's life miserable, believing that they will gain power or status in the process.
The elders of Konoha could be the main antagonists. They are often shown to be power - hungry and willing to do whatever it takes to maintain their control over the village. They might see Naruto as a threat to their authority and decide to betray him. Another possibility is Danzo. He has always had his own agenda and has been shown to be ruthless in achieving his goals. He could easily be the one behind the betrayal of Naruto in a fanfic.
It could also be that the Olympian Council as a whole acts as the antagonist. They might have made decisions that Percy sees as a betrayal, such as sacrificing the safety of demigods for their own political gain. Each god on the council, with their own self - interests, might contribute to Percy's feeling of betrayal, making the council as a whole the main force he has to oppose.
The village elders could be the main antagonists. They might see Naruto's godlike powers as a threat to their traditional way of ruling the village and decide to get rid of him. Another option could be a secret organization within the village that wants to use Naruto's power for their own evil purposes and when he refuses, they turn on him.
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.
Some of Naruto's former friends who have been influenced by the negative propaganda against him could also be antagonists. They might be misled into believing that Naruto has changed for the worse. They could actively oppose Naruto, either by trying to capture him or by preventing him from doing certain things. Another possibility is that there could be a hidden group within the village that has a vendetta against Sasuke and, by extension, Naruto for bringing him back.
Maybe the gods are jealous of Naruto's ability to inspire people. In this fanfic, they could use their divine powers to make it seem like Naruto has committed heinous crimes. His village would turn on him, and he'd be on the run. Along the way, he might discover some ancient power that can counter the gods' treachery and use it to clear his name and get revenge on those who wronged him.
A jealous classmate could be a main antagonist. This person might be envious of Naruto's popularity and his ability to make friends easily. They could try to spread rumors or sabotage Naruto's projects.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
One possible antagonist could be a jealous noble from Naruto's own kingdom who feels that Naruto doesn't deserve the prince title. This person might try to undermine Naruto at every turn, spreading false rumors about him or trying to sabotage his diplomatic efforts.
Another possible antagonist could be a fellow inmate who has a personal vendetta against Naruto. Maybe this inmate was once on the wrong side of Naruto's actions outside the prison and now sees this as an opportunity for revenge. He could try to undermine Naruto at every turn, from spreading false rumors about him to physically attacking him when the guards aren't looking.