There is always more to be said, but you may want to start with:

Why have Jews been expelled in so many countries?, answered by /u/yodatsracist

and

What did the German Jews do to make Hitler believe they lost world war one?, answered by /u/kieslowskifan

I'm not real familiar with Iron Age stuff, but most of the crappy things that happened to the Israelites/Jews (I don't know when each label is most accurate, pretty sure its a big debate) before the three Jewish Revolts (c.60-130 CE) could be generally characterized as standard political issues, though a distinct identity separate from what imperial interests wanted was frequently at the core of these political disputes. After the third revolt, Jewish political authority was shattered and decentralized and the diaspora was established; further confrontations would be with a Christianizing world.

Initial Mesopotamian Conquests The Eastern Mediterranean is a pretty important region, with trade routes linking just about everywhere--south Arabia/Horn of Africa to Anatolia, and overland routes linking Afghanistan/Iran to the broader Mediterranean world. So the first big attacks after the division of the kingdom into Israel and Judah can be seen as part of broader regional struggles--Assyrian and Babylonian empires taking harsh but not unprecedented measures against a military enemy (I can go more in to deportation as a strategy, but for just a general reference to the period Liverani's 2014 textbook is a solid overview). Non-conformity is never a desired trait in an enemy, so I wouldn't be surprised if a refusal to adopt a conqueror's religious/social practice was treated yet more harshly, but I think there are current scholars looking at how Israelite and neighboring rulers actually did actually react to the dominant Mesopotamian language and politics of legitimacy and international diplomacy. Then comes the Persian preference for autonomous vassals, everyone is happy, fast forward to Alexander the Great's Successors and you have the first instance where internal historiography sees Jews as persecuted: the Maccabean Wars (I'd argue the depiction of Assyrian/Babylonian attacks portrays them as important because they happened to Jews, but not that the attackers themselves targeted Jews differently).

Revolts against Greeks The Maccabean Wars get recorded as a harsh, religiously-motivated Seleucid persecution. The broader Syria-Palestine region was the site of Ptolemaic-Seleucid rivalry, but it doesn't seem to have been subjected to any unexpected royal interest until Antiochus IV started really pushing Hellenization. The Bible frames his actions as persecution of all things Jewish, though modern scholarship sees him as intervening in a civil war or other internal dispute in order to help his preferred (urban and pro-Greek) faction of Jews. Whatever the exact cause, this war certainly helped shape a distinct, non-Hellenic, Jewish identity. Shaye Cohen (1990) details how a non-Hellenic, but still Hellenizing, identity formed in this period; so while some political forms may have been adopted, underlying an outwardly similar set-up was a deep-rooted belief in difference. I tend to agree with him that this is a crucial part in the future preservation of Jewish identity even when politically integrated into Greek and Roman empires: to the Greeks "'common blood' became much less important, and 'common language' and 'common way of life' became much more important... [while for] the Ioudaioi... common blood remained important, common language became much less important, and common mode of worship and common way fo life became much mroe important" (p. 220). So, way of life does became a major difference, ethnic identity is preserved, and and tension remains. I'm tempted to classify the Maccabbean Revolts as still a primarily political thing, but they quickly took on a cultural/religious/ethnic role if they did not indeed stem from that.

Revolts against Romans Then come the Jewish revolts that are eventually put down by Vespasian and co. There had been a kind of uneasy tolerance before (Romans would have liked a bit more direct loyalty to the Emperor an the Imperial cult, but recognized that the hesitance was, in modern terms, a 'sincerely held belief' and not nascent treason, but they still didn't trust quite as much; Jews were always under some, if subtle, pressure to Romanize), with a couple small revolts set off by particularly disliked governors. The camel's back that broke into the Great Revolt was given its final straw by a governor desecrating the temple to steal its treasury.

After a very brutal war (my personal hunch is that the initial loss of a full legion made total, crushing victory a necessity for the Roman side), the Temple was destroyed and the diaspora began (not that there hadn't been any spread before, but the destruction of the Temple changed the nature of Jewish authority). This obviously unenjoyable experience led to another revolt in Africa about 50 years later, and one in Judea about 10 years after that, which also added to the diaspora. Despite the initial tension having religious and cultural aspects, tensions that intensified as Jewish revolts were brutally put down, I would still see the Roman responses as primarily political. Part of my opinion is based on seeing tolerance in the ancient world as allowing for judgement and distrust that I don't mean when I use the word to refer to modern communities; there were recognized differences in religion and identity that caused division between rulers and ruled, but this was not what led directly to warfare and persecutions. An explicitly religious, and not political motivation, is seen centuries late in Decius' and Diocletian's persecutions, and certainly in the Christian persecutions of Jews.

Antique Jewish Communities One final thing I'd like to address is the idea of Jews living in communities isolated from non-Jewish society. I can't speak to the nature of the diaspora in the Roman Empire, but there is actually a decent amount of surviving material documenting Jewish interactions in Babylonia (and I think a garrison in southern Egypt [Elaphantine?] is thought to be Jewish, but Egypt is not my thing). I have not read the entire book (its a decently long collection of essays), but the 2014 book "Encounters by the Rivers of Babylon: Scholarly Conversations between Jews, Iranians and Babylonians in Antiquity." edited by Uri Gabbay, and Shai Secunda is a great resource. While this does show Jews as still a distinct, identifiable group, its also pretty damn hard to find any Jews who aren't explicitly marked (such as by personal names or ethnic gentilics)--they would just look like regular non-Jews, so its always tricky to identify the less strident boundaries of a community. In general, Jews seem to have been one of many identifiable but socially integrated ethnic groups in ancient/antique society.

tl;dr To sum up, I'd see the Assyrian/Babylonian conquests as standard military/political ventures, and the tensions with Rome as stemming from problems rooted in identity but of still a primarily political nature. Up to that point, Jews did not live in truly isolated communities, and the distinct identity that would cause tension with Rome seems to have been given final form in the Maccabbean Wars, and it was this identity that allowed a Jewish diaspora, which set the stage for late conflicts with Christian polities.

Sources Mentioned

-Liverani, Mario. The Ancient Near East: History, Society and Economy. London: Routledge, 2014.

-Shaye J.D. Cohen, “Religion, Ethnicity, and ‘Hellenism’ in the Emergence of Jewish Identity in Maccabean Palestine,” in Per Bilde et al., eds., Religion and Religious Practice in the Seleucid Kingdom (Aarhus: Aarhus University Press, 1990), 204-223

-Gabbay, Uri and Secunda, Shai, eds. Encounters by the Rivers of Babylon: Scholarly Conversations between Jews, Iranians and Babylonians in Antiquity. Texts and Studies in Ancient Judaism 160. Tübingen: Mohr Siebeck, 2014.