Just as a warning, this post will have spoilers.
So I have been reading on stuff just before and after Civil War. In the New Avengers and Secret War they were building up to there being something wrong in SHIELD (and Hydra), and Iron Man was helping lead the Avengers looking into this. He talked about the problems over and over. Then, all of the sudden, he forgets all this and goes 100% behind SHIELD with the Civil War.
Am I missing where they addressed this? Did he just forget that there were problems in SHIELD (problems that would eventually come out in Secret Invasion). Did he figure, I know there is something wrong going on here and the organization is totally corrupt, but hey, I guess thats ok...
It just doesn't make sense.