My answer is "no".
Historically, anti-semitism was not an issue in the Muslim world. When the European barbarians invaded Palestine in 1099 and conquered Jerusalem, they found not only a large Muslim population, but also a thriving Jewish population. Which, of course, they slaughtered to the last man. If you are looking for the root causes of anti-semitism in the Middle East, you have to look to the Zionist movement and the frictions between Jewish settlers and Muslim settlers in Palestine in the period of British rule.
Let's start with 1900. At the turn of the 20th century the percentage of practicing Jews had fell to under 10% of the population of Palestine, mostly because it was advantageous from a tax point of view to convert to Islam under the rule of the Ottoman Turks, not because of any pograms against Jews. It is ironic, in the context of the current problems between Palestinians and Israelis, that most of the Palestinians in actuality are ethnically identical to the Israelis who they are fighting -- i.e., they're both ethnically Jewish, it's just that one group converted to Islam, while the other one did not. (Note: This is a *drastic* simplification of the situation but for the purposes of this discussion sufficient).
In any event, the Ottoman Empire fell during WWI and Britain got the Palestinian and Jordanian mandate. Now, first you must remember how Ottoman land management occurred. The Ottoman Empire was the last feudal state, i.e., a state based upon conquest and plunder. One of the things plundered was the land. The owners of the land were stripped of their ownership, and the ownership was transferred to Ottoman Turks instead. Who, as the Empire wound down, gravitated to Istanbul. The former owners of the land then ended up working as tenant farmers for absentee landlords and paying a percentage of their crops as rent to said landlords.
Anyhow, the British made the decision to respect the Turkish land titles rather than redistribute the lands to the people who had been working the lands as tenant farmers for generations. And the Zionist movement had access to capital, while the tenant farmers did not necessarily have such access. What ended up happening was that Jews moved in and bought up lands from the absentee Turkish landlords who needed money far more than they needed some land in what was now a foreign country. As far as the new Jewish owners were concerned, it was simply commerce. The historical question of how those lands ended up titled to those absentee Turkish landlords did not concern them. Where the people went who were evicted off the lands by British courts and escorted off the lands by British law officers was not a concern either, they probably figured that the displaced farmers would just find some other place to go, some other land to rent, the Middle East is a large place after all. The problem is that when you create a large landless unemployed minority, you create a population that is ripe for exploitation by ideologues. And some of those ideologues, as usual, found it advantageous to use anti-Semitism as their tool to get popular support.
Now, I am entering into a sensitive area here, because the above explanation may appear to be blaming the Zionist Movement for causing frictions with the Palestinians that eventually exploded into the current situation. Indeed there was, and has historically been since the beginning, a striking lack of consideration for the sensitivities of those pushed off of their traditional lands as a result of either the pre-1948 activities of the Zionist Movement or the expulsion of a large segment of the Muslim population in the time frame immediately following the foundation of the state of Israel. There was no thought to their fate and no thought to helping them find a new home elsewhere in the region, either by the new Jewish immigrants or by British officials or by any of the post-independence nations in the region. If someone, anyone, over the past seventy years had taken in the displaced population and given them citizenship in some state, any state, there would be no "Palestinian problem". Rather, after a few generations as a full citizen of some other country it would be like the situation of Irish-Americans, who might have a propensity to visit Irish pubs and drink beer on St. Patrick's Day but otherwise are culturally indistinguishable from any other American and no more prone to blowing up the occasional London subway station than any other American.
However, it can be said that there was little leeway for the new Jewish immigrants to do much beyond what they did. It was more a case of, "we're being persecuted in Europe, we need this land as a refuge, we will do what it takes to obtain this land, and people who already have this land are simply out of luck." All available resources were being used to relocate Jews to Palestine, there simply wasn't anything left over for addressing the fate of the tenant farmers who formerly farmed their new lands, even if the mindset had been there (which arguably it was not -- my conversations with ardent Zionists tend to end with a statement from them along the lines of, "we are the most persecuted people ever, people less persecuted than we have historically been simply have no reason to complain about anything bad that happens to them" -- an attitude not conducive to any sort of diplomacy or smoothing of ruffled feathers). The location of most of Europe's Jews in 1947 should be instructive there -- most of the surviving European Jews in 1947 were in exactly the same concentration camps that Hitler had placed them in, except renamed to "relocation camps" and with the guns facing outward to protect them from Europeans who wished to finish the job Hitler had started rather than inwards.
But back to our story... so anyhow, the point, the point... ah yes. A large population of displaced people. Ideologues like the various Arab dictators in the surrounding states who find it useful to use this large population of displaced people as pretty much slave labor and as a way of distracting their own population from the failures of these dictators. People like Yasir Arafat, who invented the concept of a "Palestinian" and made corrupt deals with said dictators to make sure that his new-found "people" didn't get citizenship and thus assimilated out from under him, then, when that scam started running dry, managed to make a corrupt deal with Israel to set him up a Bantustan-style apartheid state on the West Bank and Gaza Strip in exchange for "peace" that any sensible person could have seen wouldn't happen because if there was peace, then the corruption of the Arafat regime and its utter lack of empathy for the plight of the population it supposedly ruled would come to the forefront. All of these people found it handy to fan the flames of anti-semitism in the Middle East, and the new European immigrants to Israel didn't help the situation either, refusing to learn the language of the nations that surrounded them and having utterly no interest in engaging with non-Jews in any way. (The percentage of Jewish-faith Israelis who speak Arabic is still astoundingly low, considering that Israel itself still has a large population of Arab citizens). As a result, Israel is now the most dangerous country in the world in which to be a Jew. While violence against Jews in other parts of the world has become almost unknown, it is an almost daily occurrence in Israel.
So now we go back to the question of whether there is any inherent reason for anti-semitism in the Middle East. I would say that any relatively affluent largely-European population pushing a largely-Arab population off of the land of historic Palestine would have been similarly demonized by the surrounding states. That is, that it isn't anything about being Jews that is the root cause of the frictions between Israel and its neighbors, there would be anti-Christianism (is that a word?) if it had been Christians who had instead seen the opportunity of buying cheap lands from absentee Turkish landlords and bought up the place. In short, what we are seeing in the Middle East today may be being expressed as anti-semitism. But what it is, in the end, is whatever happens when a more successful culture collides with a less successful culture -- the people in the former get demonized by the latter.
And there ends my history lesson, and the end of my explanation of why I believe anti-semitism is not inherent in the Middle East.
-- Badtux the History Penguin