It appears as though the criteria was based primarily on wins and losses in the past decade -- not heartbreak, off-field shenanigans or the emotional wringer of QBs who just like to have fun out there -- which makes the Vikings' victory more impressive.
From the Business Journal:
The Vikings ranked as the 30th most difficult team to cheer for among all of the 122 teams in the four major professional sports after finishing seventh among the NFL's 32 teams. That was the highest mark among local teams, and this is one list where you don't want to be at the top. On Numbers based its rankings on the principle that a perennial loser is harder to root for than team that consistently wins.
The Wolves ranked 37th overall, the Wild 56th and the Twins 76th. The Washington Nationals were the hardest team to root for -- finishing slightly ahead of the Detroit Lions.