I second the idea of exploring the expelledexposed.com website. There is a lot of information, separating fact from fiction, on the scientists featured in the documentary.
I am not immersed enough in the scientific world to personally attest to any persecution of scientists researching or advocating intelligent design but I can imagine it would be difficult to hold these views in the scientific community. However, there are a LOT of half-truths and false implications and outright fiction in the documentary and it troubles me that many of these things go unquestioned by viewers. Before I get flamed
let me add that I don't think false representations are uniquely made by the religious - in no way am I suggesting that or trying to offend anyone.