Well, it's recognition that they've had a pretty darn good decade, wouldn't you agree? So yeah, I guess I consider it a nice honor.
Of course no intelligent, serious publication could name any team besides the Patriots and Red Sox as teams of the decade in their respective sports. The Steelers could make a case if they won this year's Super Bowl (not likely) and the playoff-bound Yankees, Angels, Phillies or Cardinals could challenge the Red Sox if they win the upcoming World Series.
It's premature to release these types of lists right now since the 2009 seasons are still ongoing - (not to mention the fact that the decade really doesn't end until 2010, so I assume they are using 2000-2009 which is not accurate) but at this point in time, there's really no debate in football or baseball.