My esteemed friend and frequent contributor on this blog, Jonathan Prejean, has uncovered some delightful information about the ancient Scottish Armstrong and Elliot clans, who inhabited a land just north of the border with England. And, lo and behold, we may even be relatives somewhere down the line (I met a nice fellow at the booth for Clan Elliot at the yearly Highland Games in metro Detroit a year or two ago, and he explained to me how his clan and my own were closely related).
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The ancient Armstrong fatherland.
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My own (partial, tentative) theory of the strong Scotch-Irish connection to anti-Catholicism is one of historical / sociological causation. Some of the Protestant Scots migrated to northern Ireland where they were a minority among the Catholic native Irish. So they were in the majority religion in terms of the British Isles as a whole, but a minority in their adopted home. This led to a curious and peculiar "inferiority complex within a 'superior' mentality", perhaps leading to some of the unfortunate characteristics of the exceedingly ugly and ignorant anti-Catholicism that we see in action even to this day in troubled Northern Ireland.
Ancient Elliot Tartan
When the Scotch-Irish migrated, in turn, to the southern states of America, their religion (and anti-Catholicism) dominated the landscape. Since there were few Catholics around, it hardened (helped by strong Nativism and Know-Nothing movements and racist, anti-Catholic groups such as the Ku Klux Klan) into what we see today. But thankfully it seems to become more and more marginalized within Protestantism as time goes on.
Like I said, just a speculative theory . . .