Wow, this is amazing. There were SO FEW of these counties? I guess that this was one of the elections where the lowest numbers of counties swung the other way compared to the previous election... Someone needs to check this.
Many were "spoiled" by Nader. I'm working on Gore 2000/Bush 2004 counties right now. The number is much higher, and drastically so in the South.
These few Bush/Kerry counties were in large part where Nader did his damage to the Democrats. Places like Missoula or Lincoln/Waldo, ME, or the several counties in Minnesotta are clear examples of this. If you had a swing map of census areas in Alaska you would see a few of these I imagine given Nader's strength. In many cases where Nader was strong was where Bush was not strong anyways, or there would be more of these counties. The Gore/Bush 04 counties are generally going to be where Nader wasn't strong in 2000, thus many of them in the South.