From what I understand, Tony Stark was Captain America's counterpoint in the Civil War that happened in the comics.

Not being a comic reader, I have to go by what I've gleaned from others, and I think that was related to the Mutant Registration Act, something the movies couldn't do on account of X Men being with another studio.

So, there's a reason for Tony Stark to be there.

I may have to watch the movie to find out the exact nature of the conflict.