The great cities dichotomy exists mostly because of one thing: people wanted it that way. Thomas Jefferson managed to move the national capital to a swamp in Virginia from its logical place in New York City because his vision was of a nation of yeoman farmers, free, rural people, and a government of tricky cityfolk from the north wouldn't suit his plan at all. (His federalist opposition, in contrast, was much more cynical about the ability of the people to truly govern themselves.) It's important to realize how revolutionary this idea was: rather than allowing the elite - either the aristocrats or the intellectuals to run the nation, Jefferson (perhaps naïvely) thought that a self-taught, literate citizenry would develop outside the cities, and that the U.S. would grow to be truly free.
A lot of other nations explicitly imitated the American example - the capital of Turkey was moved from Istanbul to Ankara because of Atatürk's desire to build a modern, westernized nation, with the United States as an example. No doubt many other young nations held the same idea when choosing the location of their governments.
Even in circumstances in which the United States wasn't deliberately chosen as a model, the basic reasoning remains the same. A capital in the city's economic and cultural center means that these powers would be too united. The idea is very typical of 19th century democracy: to keep a nation free, it is vital to ensure that the great powers that inevitably would rule its economy would not also rule its government. Capitalism is all well and good, but it can't be permitted to turn into aristocracy. Thus it is mostly in older nations that governments have remained coupled to their cultural centers.
Many would argue, however, that it hasn't been enough, and that the corporate powers and the true power behind most modern governments is wielded far too often by industrialists and corporate leaders - that the aristocrats rule modern societies again. Clearly in modern times more than geographical separation is needed to maintain the independence of our leadership. Perhaps we'll see a new wave of revolution in this century as a result.