I'm not sure what specifically makes you think people view it as a "Muslim/Jewish conflict". It's quite true that there is a strain of discourse that runs through the conflict as a religious one, but that is likely a more recent phenomenon inspired by the rise of religious militant movements like Hamas in the 1990s and onwards, as well as the use of religious Muslim rhetoric from Arab states surrounding Israel and Palestinian leaders in the past (despite their secularist leadership). The conflict also is muddied by the fact that "Muslim solidarity" by majority-Muslim states has historically meant that states beyond just Arab ones have refused to normalize relations with Israel or recognize its existence (or right to exist).

However, this has historically and generally been viewed as a conflict between Jews/Israel and Arabs/Palestinians (depending on the period). This is true both in views of historical newspaper records, and also in polls.

Consider, for example, articles written about the conflict in 1948 in the New York Times. Articles carried headlines like "The Two Worlds of Palestine: Arabs and Jews, deserts and fertile farms, ancient ways and progressive ideas -- these make up the Holy Land today", dated May 16, 1948. Another, reporting on the civil war and dated April 16, 1948, was titled "Jews Press Arabs in Pitched Battle in Northern Palestine". This is the theme you'll find throughout these articles.

The same is true of reporting by the Jewish Telegraphic Agency at the time, which declined to paint the conflict as a Jewish-Muslim conflict. Articles such as "Powers Call on Jews and Arabs in Palestine to Establish Truce; Arab Answer Due Today" dated March 16, 1948, and "Bevin Reported Proposing New Palestine Partition Plan to U.s.; Wants Negev for Arabs" from May 30, 1948 (Bevin being the Prime Minister of the UK at the time) make clear the view that the conflict was between Arabs and Jews.

The Christian Science Monitor was no different, either. Articles reporting on the UN Partition Plan's passage reported on "Arab-Jewish reconciliation" and "Arab-Jewish rapprochement". Reference to Muslims specifically is made in the context of French concerns about whether supporting a Jewish state's creation would harm France's ability to control Muslim-populated areas in Northern Africa, but the conflict remained painted as "Arab" on one end and "Jewish" on the other.

Polls, as I mentioned, also back up this framing. Polls through 1982, as reported in "The Polls: Attitudes Toward the Arab-Israeli Conflict" in Public Opinion Quarterly by Connie de Boer frame the question and conflict as between Israel and the Arab nations, or Israel and the Palestinians, or Israel and the Arabs, generally speaking.

So why the Muslim-Jewish conflict framing at all? As I mentioned, it's in part because of the way Muslim-majority states have joined the refusal to recognize Israel and popularity has painted it as a Muslim-solidarity conflict (a factor highlighted, as I mentioned, in the French comments in the Christian Science Monitor). There were certainly politicians who made the comments that the conflict was a religious one, primarily, which also muddied the water frequently over the years. Yasser Arafat, for example, was taped in 1994 calling for a "jihad to liberate Jerusalem" (though he claimed later this was meant in the peaceful sense, this term carries Islamic connotations as well as Arab ones to many uninformed viewers). At the same time, however, said speech reportedly (1) included the quote that the fight for Jerusalem is "for all the Muslim nation", (2) included a quote saying "What they are saying is that [Jerusalem] is their capital. No, it is not their capital. It is our capital. It is the first shrine of the Islam and the Moslems", (3) made reference to Muhammad's treaty with Koraish, and (4) closed on the note "We are in need of you as Moslems, as warriors of Jihad" (though warriors of Jihad was stated as "mujahideen"). This was not the first or last time the conflict was stated as one between Muslims and Jews by the Palestinian leadership. Fatah, the group that Arafat headed, is indeed secular and has been for awhile; much or all of the PLO, which Fatah leads/led primarily, was likewise secularist or even areligious historically. Yet the Palestinian Constitution, primarily written by Fatah's leadership in 2003 (skirting the 20 year rule for a moment), included a provision saying that Islam would be the official religion of Palestine, and that "The principles of Islamic Shari’a shall be the main source of legislation". Hamas, founded in 1994, wrote its charter with goals as creating an Islamic state and implementing Islamic law, with a preamble quoting a Muslim Brotherhood leader saying "Israel will exist and will continue to exist until Islam will obliterate it, just as it obliterated others before it", and provisions such as "The Movement's programme is Islam", and "The Islamic Resistance Movement believes that the land of Palestine is an Islamic Waqf consecrated for future Moslem generations until Judgement Day". This is not exclusive to Palestinian leaders either. While the founder of the Revisionist Zionist movement (Vladimir Jabotinsky) wrote that creating a Jewish state would not bring Britain "into conflict with world Islam", ironically an alternative view was put forth by Judah Leon Magnes (an advocate for a binational state, not a Jewish or an Arab state, in 1930) who wrote that the balance was not between Jewish and Arab communities in the area but between "Jews and Judaism on the one side, and the Arab peoples and even all of Islam on the other." But Israel was also conscious of its desire to make good on relations with various Muslim-populated states (like Iran, Turkey, and the like) so it was sometimes more wary at the high-leadership level of painting the conflict as a religious one (though some religious Jewish leaders, who have also inspired religious political parties, have certainly done so aplenty).

Jerusalem, a focal point for a lot of fighting, is a religious site holy to three faiths, making it easier to also interpret the conflict as a religious one between Muslims and Jews, since Christians have been a small minority in the conflict itself (and not always fully aligned with Muslim Arabs since not all are Arabs, especially if you look at foreign Christian groups with views on Israel like evangelical ones of course). It's also important to note that Israel, at times, has treated the conflict as one against Muslims primarily, but often in more quiet statements: Israel, for example, was willing to ally with Lebanese Christians in the Lebanese civil war because it viewed them as friendlier to it, a view that is demonstrated even by the words of Israel's first Prime Minister Ben-Gurion himself, in a discussion with his military leaders in May 1948.

These factors have to be coupled with a certain level of historical/geopolitical ignorance in common discourse. That's not a knock on people's intelligence at all, but it's important to remember that the world didn't always have a ton of information at its fingertips, and even today that availability of information does not equal attention to that information. Thus people might only have heard snippets that framed the conflict, as I imagine you're alluding to, as one continuing from "thousands of years" of conflict over Jerusalem, or between Jews and Muslims, which is not the case (that's not to say that relations have been smooth between the two, but the Arab-Israeli and Israeli-Palestinian conflicts are not a continuation of past conflicts in that sense). The Middle East is a complex beast, and hard to follow even in the best of times. Thus, it makes sense that the conflict, which has religious, ethnic, national, and wider geopolitical angles to it (all of which are intertwined), might be simplified too much to only one of them (since how people act in the conflict is too complex to categorize even on a national or ethnic basis).