The Bill of Rights was originally conceived to deal with the relationship between the State and Federal government. Only after the 14th Amendment does the notion of the individual citizen come into play, because it was through the 14th Amendment that the Federal gov’t was able to trump the State gov’t through the notion of individual rights. Probing the causes of an issue like this always leads to many different causes working in concert, and I’ll do my best to put some of the various factors into as cognizant and relevant an order as I can:
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Expansion of Rights. The history of rights is pretty interesting. They started out as privileges that nobles enjoyed and were gradually expanded to encompass larger and larger groups of people. When the American Republic was founded, rights that had come to encompass land-owning men were further expanded to all free men over 21. However, poll-taxes prevented certain classes of people from exercising various rights, such as the right to vote. Naturally, this created a great deal of tension between those who possessed rights in theory and those who could actually enjoy the benefits of said rights.
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Industrialization. Between the founding of the Republic and the 1860s, America industrialized heavily. Industrialization creates huge pressures on a society, pressures that are distinct from those of an agrarian society.
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Immigration. Between 1841 and 1860, there was a 600x increase in Immigration, and many of these immigrants were from cultures distinct from those that had initially settled America.
All of these create huge pressures that lead to the shift away from a civic republic and towards a procedural republic. While rights were always, in practice, held by a select class of people, the goods valued by that select class and the average citizen were generally in agreement because they came from the same cultural narrative. It doesn’t matter whether the individual citizen can vote if the elected government behaves as though the citizen had voted them in. As the original culture bifurcated into the new industrialized north and the old agrarian south, that could no longer be said to be the case. Furthermore, there was an influx of people such as the Irish, Germans, and Italians (to say nothing of the Mexicans that had recently been incorporated and the Asians who began migrating in large numbers in the late 1850s) who held different cultural narratives and different goods from the WASPs that had previously dominated America. Prior to that event, if a state wanted to have a recognized religious status it could (and, indeed, many did) but as soon as a plurality of religious backgrounds is established such a position becomes less and less tenable.
This all came to a head during Reconstruction because there was the introduction of a large new group of people with recognized rights: freed slaves. One of the Northern strategies during Reconstruction was specifically not to disenfranchise the African American population to help remove the old order that had dominated the Antebellum South. But the Southern States couldn’t be counted on to ensure this would happen, so it fell to the federal government as opposed to the states to ensure that individual rights were respected. This bounced back to the North, where the rights of the new classes of immigrants also had to be now respected.
The introduction of the income tax in 1861 was also vital (factor #4), since it slowly made poll taxes less necessary and less justifiable, thereby enfranchising larger and larger portions of the population, all with different and unique cultural narratives.
While these trends were interrupted in the South after Reconstruction ended, they continued in the industrialized North. Since the South remained agrarian, it was relatively unattractive to immigrants and the disenfranchisement of the African Americans returned it to a unified cultural narrative amongst those who counted.
But things didn’t really heat up in the North until 1897 with Allgeyer v. Louisiana, where the current (and broad) interpretation of the 14th Amendment was adopted and the trend of the Federal Government protecting citizens from the individual States became the norm and rights based jurisprudence that was neutral towards ends became de rigueur.
America had become a nation where common narrative of the good had become impossible. The division between the industrialized North and the agrarian South set the stage for two distinct visions of how the republic ought be managed. In the North, the pressures of industrialization and immigration lead to an atomization of the concept of rights, where individuals stood in opposition to the local power and it was the duty of the Federal government to protect the individual from the local power. In the agrarian South, it was the duty of the local powers to ensure a continuity of culture, aligning a particular sub-set of the population with the good and trying to prevent that community from being contaminated by undesirables.