One might be worried if one's favorite team couldn't beat other good teams and instead feasted on cupcakes. One would be very wrong to be worried about such a thing:
Five of the nine champions this decade posted losing regular-season records against opponents that were .500 or better, including the 2008 Phillies (43-46) . . . Conversely, teams that excel against tough opponents tend to flop in the postseason. Not since the 1995 Braves has the team with the best record against .500-or-better competition won the World Series that same season.
The article doesn't speculate about why this might be. Coincidence is almost always the best answer when one encounters weird and/or counterintuitive stats like this, but chalking stuff up to coincidence is boring, even if accurate. Because of this, let's concoct an untestable yet moderately-satisfying hypothesis: Due to the 162-game regular season, teams that win the World Series are, by definition, marathon winners, not sprinters, and the mark of a marathon winner is somoene who knows when to conserve energy and when to put the hammer down. This is not to say that teams roll over for good competition. Indeed, as the article notes, the winners play even the toughest competition at something just less than .500 ball, which ain't too shabby. It's merely to suggest that on some subconscious level, the best teams know that all wins count for the same amount during the regular season and that it simply takes less energy to beat a bad team than a good one and act accordingly.
Alternatively (though sort of relatedly), like a distance runner, they simply keep a steady pace all season long, never getting too high, never getting too low, and the strength of the competition dictates how the records fall out.
Either way, the Yankees and their fans may now feel a bit better about their inability to beat the Red Sox this year.