http://www.cnsnews.com/news/article...dd-komarnicki-i-pray-during-and-after-i-write
NTSB none too happy being cast in the role of villains, but the screenwriter's angle is the effect of the investigation on Sully.
Reading the wiki article on the incident, there was some issue with the computer sim vs. real life, which is really the main thing focused on in the movie.
As for the NTSB and feelings getting hurt, they'll get over it. Not like anyone's going to lose a job or something and compared to, say, the TSA, the NTSB's image is doing fine.