Which ones? They have a different set of fans every year.
Reading the story it seems their main criteria for judging fans is revenue i.e. how much do fans spend on the team? With that in mind it's easy to see how the Cowboys ended up in first place; they have a brand new stadium with massive capacity, hugely expensive seats and it's usually sold out as well. Look at the rest of the Top 10 and you see a similar trend of expensive tickets and/or sold out stadiums; Giants, Jets & SF all have a new stadiums with expensive seats, Indy's stadium is older but not by much while New Orleans' stadium was renovated in 2011. New England and Baltimore are among the most expensive tickets in the NFL, and Green Bay and Chicago both have massive waiting lists.
The ranking is even called the "NFL Fan Equity ranking" so it's less a ranking of quality fans and more a ranking of which fans can afford to spend the most on their respective teams.
Yeah, that fact that the Seahawks and Chiefs are 26 and 27, despite the fact that they have been dueling for the loudest stadium for the past couple years is a huge indictment on the study IMO. The Cowboys stadium seems to be just as loud for the opposing team half the time, yet they are the most passionate?