When the "sides" for Captain America: Civil War were first revealed through promotional material, it was a little odd to see Scarlett Johanssen's Black Widow on "Team Iron Man". Natasha Romanov's relationship with Tony Stark was always tenuous at best, and Captain America: The Winter Soldier helped to cement a stong brother/sister relationship between Steve Rogers and the former Russian agent. Producer Nate Moore revealed that the storytelling reasons go in tandem with Natasha's character progression, even if it seemed to against her friendships.
"...Black Widow teaming with Iron Man. I think it was unexpected even for us but as we talked about it from a storytelling point of view, it really made sense because I think Black Widow is more pragmatic than we give her credit for," Moore said. "And sometimes she's looking at the solutions from a different angle than Tony Stark [aka Iron-Man], who's very emotional. Even though they don't react to the same things, in the same way, their conclusion that they came to ended up being the same. So it really was talking each character through like that to figure out who would end up where."
Given that most of Natasha's character development has involved escaping the shades of her dark past, it makes sense that she might side with Tony as a means of atonement for her actions as a former spy. In addition, much of the information surrounding her past was leaked when S.H.I.E.L.D. collapsed, and so choosing to rebel against yet another government with Steve would probably not do her any favours.
Captain America: Civil War releases May 6th, 2016.