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You're right, the main rivalry is with Arabs, not with Israelis (even though they are both Semitic people and ultimately in the same bag from a Persian point of view).
The problem of Persians has always been to be an Indo-European people sandwiched between Semitic people to the south and Turkic people to the north, both are considered historical enemies that can't be trusted (and the recent Iran-Iraq war, started by Iraq, has done nothing to change that opinion). To add to the ethnic divide, Persians have developped their own branch of Islam while Semitic and Turkic people are almost entirely sunni muslims. Iran feels relatively safe only on its eastern border with other Indo-Iranian countries.
The anti-Israeli rethoric is failry recent indeed, too recent to be genuine. In my opinion, the main goal of that posture is to look sympathetic to Arabs, to be perceived by Arabs as a potential ally against Israel, to convince Arab countries that Iran's nuclear program is not a threat to them but only to Israel and should therefore be supported.
Ultimately i don't think Iran gives a damn about Israel (other than it's Semitic people who can't be trusted), the real enemy are sunni muslims and that's who the Iranian military program is primarily aimed at.
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