Goodell wasn't commissioner when Super Bowl XL happened. He became commissioner about seven months after that game.
There was a woman who grew up in the same town in Maine where I grew up, and she was a friend of a bunch of my friends. She was a Patriots fan because, well, Maine, and she was also a Saints fan for some reason (I'm not criticizing - I grew up in Maine and I was the only Seahawks fan I knew). I asked her how she felt about Goodell, given how much he had always helped the Patriots, but harmed the Saints. She agreed with me on both points and strongly disliked Goodell even though he's basically been Kraft's guy in the NFL office.