Bush had much less appeal in the Kerry counties, on average, than Kerry did in the Bush counties.
I was thinking about this one, and I'm not sure you're right. Thinking about it, I would say that in a close election, the person whose votes are distributed more "efficiently" can win the electoral vote and lose the popular vote.
This is what happened with Bush in 2000. Gore won the popular vote, but his votes were concentrated more in places where he was very strong, whereas Bush's votes were spread out among more states that were carried with smaller margins (excepting the thinly populated mountain west).
This time, the results were reversed. A swing of 65,000 votes in Ohio would have allowed Kerry to win the electoral college even while Bush had a popular vote margin 7X bigger than Gore's margin in 2000. This suggests to me that in general, Bush carried his states more strongly, while Kerry penetrated into a larger area relative to his vote count. This is borne out by the fact that while Bush's vote total increased significantly from 2000, his electoral vote count did not. Kerry almost maintained Al Gore's electoral vote count, with a smaller share of the popular vote relative to Bush. It seems then that this time, Kerry had a more efficient distribution of his votes, which translates into less appeal in the Bush states than Bush had in the Kerry states. (I hope this all makes sense!).