Maybe Peter has some kind of spell or technology that hides his identity from Tony specifically. In the fanfiction world, there could be all sorts of magical or high - tech explanations. It could be a device that scrambles Tony's perception of Peter when he's in his Spider - Man guise.
One possible reason could be that Peter is really good at hiding it. He's careful with his actions and words around Tony, so Tony just doesn't suspect. For example, he always changes out of his suit before meeting Tony.
This situation can create a lot of opportunities for character growth. For Peter, he has to keep this huge part of his life hidden from someone he respects like Tony. He might struggle with the lies and the secrecy. For Tony, when he eventually finds out, it could be a shock that makes him re - evaluate his relationship with Peter. He might feel betrayed that Peter didn't trust him enough to tell him, or he could be impressed by Peter's ability to keep such a big secret.
One reason could be that he's on a dangerous mission. Peter might think that his enemies could use Mary Jane against him. So, to protect her, he decides to keep his distance. For instance, if a powerful villain has threatened to harm those close to Spider - Man, Peter would rather stay away from Mary Jane to keep her out of harm's way.
One possible reason could be that Tony has some pre - existing biases. Maybe he has a set idea of the type of person he wants on his team and Natasha doesn't fit that mold in his mind. For example, if he's looking for someone with a more technical background and Natasha's skills seem more combat - oriented to him at first glance.
It could also be due to external pressure. The media or some powerful figures in the fanfiction world might force Tony to stay away from Peter. They could spread false rumors about their relationship or use their influence to separate them for their own gain.
Maybe Tony is a very independent person. He likes to do things on his own and get things by himself. Being handed things might make him feel like he's being treated as incapable or like a child.
It could be that Tony Stark already has a full team with specific skill sets that he believes don't need Natasha's skills at the moment. He might be focused on tech - based heroes or those with superpowers that are more in line with his current projects.
Peter might be embarrassed at first. He's been idolizing Spider - Man and now Tony, a real - life hero - like figure, knows about it. But then he realizes that Tony could be an even greater source of knowledge and support, so he becomes more open about his love for Spider - Man.
One possible plot twist could be that Peter is in a situation where he has to save the Avengers secretly as Spider - Man. Maybe they are captured by a powerful villain and Peter, using his knowledge of the Avengers' base and their habits that he learned as a fan, manages to rescue them without revealing his identity. Another plot twist might be that Peter starts to leave little hints about his identity, like using a specific web - shooting style that he once wrote about in a fan blog when he was fangirling over the Avengers. And the Avengers start to suspect there's something familiar about Spider - Man but can't quite put their finger on it.
One reason could be to create drama. Writers might think that making Spider - Man cheat can add a lot of conflict to the story, whether it's between him and his love interest or among his friends who find out. Another reason could be to explore the character in a different light. Maybe they want to show that even a hero like Spider - Man has flaws.
Power struggles can be a reason. Spider Man, being a solo hero with his own set of powers and moral code, might not agree with Shield's more bureaucratic and sometimes secretive ways of handling things, so they clash. For example, Shield might want to control Spider Man's actions, which he resists. This can lead to a fight. Also, there could be a villain manipulating events behind the scenes to make it seem like Spider Man is against Shield or vice versa.