It could be some of her jealous peers. For example, those who are envious of Sakura's skills or her closeness to certain important characters in the Naruto universe. They might spread malicious gossip about her to make her an outcast.
In some cases, it could be a mysterious figure from outside the village who is trying to undermine the unity of the village. They target Sakura and make her seem like a danger to the village, causing the villagers to turn against her.
Perhaps the elders in the village who have traditional views. They might see Sakura's new ideas or unorthodox ways as a threat to the established order in the village. So they use their influence to ostracize her.
One possible storyline could be that Sakura is outcast because she has developed a new and unorthodox ninja technique that others are afraid of. So she has to struggle alone, trying to prove its value.
One possible antagonist could be a popular girl in school who is jealous of Sakura's popularity and tries to undermine her at every turn. For example, she might spread false rumors about Sakura or try to steal her friends. Another could be a strict teacher who doesn't believe in Sakura's abilities and is always giving her a hard time, like constantly doubting her work in class or not allowing her to participate in certain school activities.
In certain 'sakura haruno revenge fanfiction', Orochimaru might be the antagonist. Given his history of using people for his experiments and causing harm, Sakura could decide to take revenge on him, perhaps to stop his evil plans and avenge those who have been affected by his actions.
There could be a powerful ayakashi leader as the main antagonist. This leader might be controlling the other ayakashi and specifically targeting Sakura Haruno for some reason. Maybe it's because of her latent power or her connection to a certain place or person. The other ayakashi would then be minions following this leader's orders in the fanfiction.
Danzo could be a great antagonist. He might see Sakura's prodigious abilities as a threat to his power and control in the village. He could try to undermine her at every turn, whether it's by sending assassins after her or trying to discredit her in the eyes of the villagers.
Another possible antagonist could be a jealous relative. For example, a cousin who believes they should be the heir instead of Sakura. This relative could spread false rumors about her, or try to sabotage her efforts to prove her royalty in more subtle ways, like stealing important documents or artifacts related to her claim to the throne.
I don't know for sure, but since it's a fanfiction centered around Sakura Haruno, she is the main focus. However, it may also feature characters who had a major impact on her life. This could include her sensei, like Tsunade, who trained her in medical ninjutsu. There's also a possibility that new characters created specifically for this fanfiction could be main characters as well, but that's just speculation.
In some Sakura Haruno alpha fanfiction, Kakashi could be a significant character. He might act as a mentor to Sakura in her new alpha role. He could guide her in making difficult decisions, like when she has to choose between the safety of the village and the life of a comrade.
Some fanfictions might introduce new original antagonists. These could be powerful rogue ninjas who are after Sakura for her medical skills or some special power she might have in that particular fanfiction. They would then be the main threats that Itachi has to deal with to protect her.
In some fanfictions, there could be a co - worker who has a secret crush on Sasuke or Sakura. This co - worker then tries to drive a wedge between them by spreading rumors or causing misunderstandings in the office environment.