Sometimes, it's just a way to shock the audience. Fanfiction authors often like to take risks and do unexpected things to their beloved characters. Torturing Natsu can be a very unexpected and extreme move that can leave a lasting impression on the readers, whether they like it or not.
One possible reason could be that Erza is focused on her own goals and career in the Fairy Tail guild. She might see a relationship as a distraction at that moment. For example, she is always striving to be stronger and take on more challenging missions. Another reason could be that she may not view Natsu in a romantic way but more as a close friend and guildmate. Maybe she has a different ideal type in mind, someone more calm and studious rather than Natsu's brash and impulsive nature.
Well, in some fanfictions of this kind, Naruto could be tortured physically by being chained up and beaten. His captors might also starve him or deprive him of water to weaken him. It could also be that they use some sort of dark magic or forbidden techniques on him that cause extreme pain and discomfort.
One possible scenario could be that he is captured by an enemy ninja group who wants to extract information from him. They might use various cruel methods like chakra - draining techniques or physical harm. Another could be that he is tortured as a form of revenge by someone he has defeated in the past.
One possible plotline could be Clary's friends finding out about her being tortured and launching a rescue mission. They might face many obstacles on their way to save her, like fighting off the torturers' guards.
One possible scenario could be that Natsu is killed in a battle against a powerful and unexpected enemy. Maybe a new dark mage appears with powers that can overpower Natsu's fire magic.
Perhaps in the fanfiction, Natsu is betrayed by someone he trusts in a mission. For example, they might leave him behind in a dangerous situation to fend for himself while they take the credit for the mission. Or it could be that a love interest betrays Natsu by choosing someone else over him due to some false perception or external pressure.
One possible scenario could be that Natsu confesses his love to a character, perhaps Lucy, and she rejects him because she doesn't see him in that way. She might think of him only as a good friend. Another scenario could be that Natsu is rejected in a job or a quest application within the fanfiction world. Maybe the guild he wants to join or the person in charge of a certain task doesn't believe he has the skills or the right attitude.
Maybe it's part of a plot to have Percy gain some sort of power or knowledge. In many fictional stories, a character has to go through great pain and suffering before emerging stronger or wiser. The torture in Tartarus could be a way to set up this transformation for Percy.
Perhaps Gray and Erza lead a search party. Gray could use his ice - make magic to freeze any obstacles in their way while Erza, with her many armors and combat skills, could fight off the kidnappers. They might also get some help from the other guild members like Wendy, who could heal Natsu if he's been injured during the kidnapping and torture.
One possible reason could be that Erza might have taken on a dangerous mission alone without informing Natsu. Natsu is protective of his friends and would get angry if he thought Erza was putting herself in unnecessary danger.