Gore did not win the popular vote by a large margin. According to Wikipedia, he was ahead a mere 543,816 (0.5%) votes. [1] It was only the third time in history that a candidate lost while winning popular vote. I don't think you should dwell on that particular point. Can you find examples in other elections where the theory falls apart?
Also, the second footnote in the essay offers the reason that Bush did not focus his campaigning on the popular vote. [2]
[1] http://en.wikipedia.org/wiki/U.S._presidential_election,_200...