That is the question and fans are hoping that it will be answered in Captain America: Civil War. Others have theorized that Peter Parker looks up to Tony Stark and that is why he wants to be part of the team. Even as a much younger Spiderman, the story line might have been laid out this way for years.
There is also a rumor out there that states that Spiderman and Captain America get into an altercation. Fans believe that makes perfect sense as to why Tony Stark would want anything to do with the character.
At first, it would appear that Spider-Man would be on the Iron Man side of things, but another source is claiming that is not the case one-hundred percent. The movie is going to tell the story, but it will be amazing if it does not leave anything out and you can leave the theater satisfied.