Although extremists in Iran are problematic for the US and Israel, Iran is not a natural enemy of the US. (Let's not forget that we supported the dictatorial Shah of Iran and had a roll in creating the conditions that led to the revolution there).
Most terrorism in the world in the past two decades has emanated from Sunni Islam, not Shiite Islam.
Iran's population is young, educated, and largely secular or semi-secular. The best way to engage and influence this generation is to befriend them, not demonize them.
It is counterproductive and not in the best interest of the US to treat Iran as an enemy. The best way to counter the influence of the extremist component of the political and religious establishment there is to make it no longer possible for them to demonize a friendly US.