There are a few layers to this:
1. As another commenter already pointed out, Iran is not an Arab country
2. It is very true that the Iranian people absolutely does not hate Jews. In most Arab capitals, simply to walk around while visibly Jewish is either risky or downright suicidal. The same is true in other Muslim countries such as Pakistan, and increasingly in majority Muslim neighborhoods in Western cities. Iran does not have this problem. In fact the Iranian and Jewish peoples share a deep bond that goes back to the time of Cyrus the great, who famously freed the Jews of Babylon in 538 BCE, and allowed them to return to their homeland and rebuild their temple. To this day, Iranians and Israelis tend to get along. For example, the Iranian diaspora is conspicuously absent from anti-Israel protests in the US, and you will often see Israeli and pre-revolutionary Iranian flags flying together in anti-IRGC "Free Iran" protests (to the dismay and confusion of pro-IRGC protesters).
3. The current islamic government of Iran - the IRGC - has historically persecuted and executed Iranian Jews, especially in the early days of the revolution. There is a reason so many Iranian Jews live in the US... It is true that they have not implemented a Nazi-style policy of total eradication of their Jewish population, even though their foreign policy is entirely built on total eradication of Jews abroad. But let's be clear: Jews in Iran live in a state of submission and fear. In theory the IRGC is "anti-zionist" and not "anti-Jewish"; in practice the difference is blurry and arbitrary: Jews are eternally suspected of duplicity and disloyalty, and must continuously prove that they are not secretly "zionists". When Iranian Jews make public statements criticizing Israel, they are doing so because of this pressure from a totalitarian regime, and their safety depends on it. A statement by the Jewish community in Iran only reflects what the IRGC wants them to say. A useful comparison is Soviet anti-zionism, which followed similar patterns: Soviet Jews often denounced zionism loudly and publicly, and from the outside it appeared that Jews were a "protected minority" living peacefully. But ask Jews who actually lived in the Soviet Union at the time, and you will hear a very different story...