Take a look at a world map in order to understand why Iran is a bit worried. They are practically surrounded by American troops. I don't think the Iranian people have anything against us as Americans. What I do think is that with American troops so close, it might be best to wave a saber like nuclear power to at least make them feel more substantial in our eyes.
And also keep in mind that their president, Mahmoud Ahmadinejad, was elected by the people of Iran. But he is mostly a figurehead and the country, a theocracy, is ruled by the Supreme Leader. The president shares some degree of power with the Supreme Leader, but does not have the range of influence that presidents have in more democratic societies. So when Ahmadinejad shoots off his mouth, take it with a grain of salt.
That doesn't mean that Iran is any less of a threat, especially when it comes to influencing neighboring countries like Iraq.
But I certainly don't think threatening Iran serves them or us or the world any good. We should learn a lesson from the Iraq fiasco.