The United States has had geographic advantages that have allowed it to flourish that other states have not. By being in the New World, we didn't have to worry about deposing a king that we lived with (such as in France), and we didn't have any immediately threatening neighbors. Being separate from Europe, we also had the ability to establish something instead mostly new instead of going through the slow process of transformation (such as in England).

You make an interesting point about leaders' fear of the intelligentsia. I suspect that scientists and philosophers present new technologies and new ideas. Both of these are threats to power and business (I mention business because it is my observation at work that new ideas and technologies are threats to running things easily and cheaply).