Before the civil war was Captain America and Iron Man best friends. I've always thought of them  to have the same friendship as Superman and Batman (Bruce Wayne) have. Anyway let me know what your opinions are.

Yeah. Civil War changed a lot of things. I was hoping to see Iron Man & Captain America ( Steve Rogers ) getting back together and resolving their issues. But no such luck, the Avengers simply reformed, with Steve and Tony only saying a few words to eachother, without any real conclusion at all. I guess they might 'come back together' in Avengers: Prime, but right now it would seem the relationship between Tony and Steve is anything but an attempt to regain their friendship. They work on the same side, but that's about it.
While you could indeed call them somewhat of 'best friends' before the Civil War.

You got it right, Steve, Tony, and even Thor were the best of friends even looked at each other like brothers and like brothers they had their disagreements (putting it midly). I am not sure what's going on or what happened with Avengers Prime but I think they will eventually forgive each other. Its been hinted at in a few of the titles after Steve's return and the end of Dark Reign. Especially between Tony and Thor, but its not one of those things that can easily be forgiven.