I'm going to side on the fans' side of the issue.
If I was to go to the SB, pay outlandish fees to get there, only to be sent to a downgraded section, or a bar to watch the game, I'd want a bit more than the NFL is offering. Not only would a person have to be compensated for the costs surrounding getting there such as travel and a hotel, but the actual time involved in the useless endeavor. I am sure many of these fans had to take time off from work they cannot get back, which cost them as much, or even more than the tickets & trip itself.
And that doesn't take into consideration the sheer aggravation of being screwed over by the NFL. According to the Times article, the fans got the shaft pretty bad.
I'm not saying that they need something extravagant, but I think somewhere around $10,000 per person from Jerry and Roger Goodell's pocket would be good compensation, as well as an in-person apology from both.