The nuclear program is not the only issue dividing Iran and the US. Iran's role in the region is also creating conflicts. For example, you support the Shiite Houthi militias in Yemen whereas the US is on the side of the coalition led by Saudi Arabia.
First of all, there are Persians and Arabs. The fact they share a religion, a Shiite religion, does not mean that they're close. It doesn't work that way. There is a relationship because there is a long border. There is going to be trade between them. They should have a relationship. They want to make sure that - though, that there is no undue influence coming from Iran or any other country in the region.
Iran of course is Shiite, while the bulk of the Arabs are Sunni, that is a problem or could be a problem. Also, there is the simple fact that Iran is non-Arab and most of the Muslims in the Middle East are Arab.