Well, it's possible that a powerful and evil pirate lord could be the main antagonist in 'hermione is a pirate fanfiction'. This pirate lord might control a large part of the seas and sees Hermione as a threat to his dominance. He could have a large fleet and many ruthless henchmen. He might try to capture Hermione to either make her join his crew or to simply get rid of her because she is disrupting the order he has established in the pirate world.
It could be the navy. They see pirates as outlaws and would be determined to capture Percy and his crew. They might have better - equipped ships and more trained soldiers, making them a formidable foe for Percy and his fellow pirates.
One potential main antagonist could be a powerful pirate captain who sees Harry as a threat to his control over the seas. Maybe this captain has some dark magic powers as well.
The traditional wizarding authorities could be antagonists. Since Fem Harry Potter is into pirate stuff which might be seen as unorthodox in the wizarding world, they could try to stop her from following this new path.
The Ministry of Magic officials who strictly enforce the marriage law could be antagonists. They might be so bent on following the rules that they don't consider the individual feelings of Charlie and Hermione. For example, an overzealous bureaucrat who keeps checking on them to make sure they are fulfilling their marital duties according to the law.
It could be rival mercenary groups who see Hermione as a threat to their business. They might try to undermine her at every turn.
The main antagonists could be other pirate crews. There might be a particularly ruthless pirate captain who wants to take over Percy and Annabeth's ship and all the treasures they might be after. This captain could be jealous of Percy's powers and see him as a threat.
The Ministry of Magic itself could be an antagonist. If they don't approve of Hermione's adoption due to her age or some bureaucratic reasons, they could try to take the baby away. They might think she's not fit to raise a child, which would create a lot of conflict in the story.
In this fanfiction, apart from Voldemort, there could be some dark wizards who are working independently but have the same goal of seeing the Potters dead. They might be jealous of the Potters' popularity or have some old grudges. These dark wizards could be in league with Voldemort or acting on their own, and they would be a big obstacle for Hermione as she tries to save the Potters.
One possible main antagonist could be a dark wizard from the past who senses Hermione's interference in the timeline and tries to stop her. This wizard might be afraid that Hermione's actions will change history in a way that will end his power or influence.
Often, the goblins can be antagonists. If they have their own motives that conflict with Harry and Hermione's, like protecting a dark secret in the vaults or trying to take advantage of the situation for their own gain. Another possible antagonist could be a Death Eater who has infiltrated Gringotts to either steal something important or to ambush Harry and Hermione.