Strongly influenced by Marx whose dialectical materialism he rejected, Weber developed conflict theory, and social stratification theory on the basis of property, power, prestige, age and gender--all in a white European context of the 19th century. Besides class, status, gender, ethnicity, race, and prestige, the immediate and extended family structure, the ego and desire to affirm/validate the self by claiming separateness from the other may be contributing factors to the hierarchical mindset and practice. But the irony remains that in society and in hierarchies the ideal aspiration is egalitarianism.
Food gathering communities operated under egalitarian/communitarian conditions that reflected their needs and no doubt considered it "natural." Today such conditions appear antithetical to humans that respond to hierarchical models in daily life. If universally immersed in hierarchical models, why do human beings pay homage to egalitarianism (spiritual or humanist) and seek it as an ideal? Before Judaism, Christianity and Islam, paganism which was based on nature and female deity worship evolved toward patriarchal and hierarchical structures with the stratification of society owing to private property and military conquest.
Initially rooted in hierarchy of nature and then reflecting patriarchal social stratification, paganism reflects the convergence of the real and the ideal. By contrast, Christianity, once it separates people into "good and evil" dichotomy, judges all who are "good" (saved) as equal in the Kingdom of God, while the eschatological model of Hell certainly makes liberal use of hierarchies as Dante dramatized in his ingenious novel intended to criticize secular and spiritual hierarchies in the Italian city states. Of the Eastern religions, Confucianism of course is hierarchical. Hinduism, Buddhism, and Taoism are closer to paganism in spirit and structure, while they embrace a holistic oneness de-emphasized in the hierarchical mindset.
The basic hierarchic model has remained in tact throughout history partly because it reflects the stratification of "civilized society." Today hierarchies are not only present in military, government, business, hospitals, academic institutions, NGOs, but even in community groups that begin with some kind of egalitarian structure but quickly abandon it. Communist countries never managed to put into practice an egalitarian structure as their followers hoped. After taking power, they tried to address the larger issue of social justice within the context of the regime's political perimeters.
By adopting a rigid hierarchical structure to enforce "social justice," Communist regimes lost the PR war to Liberal-bourgeois regimes that idealized the individual within the hierarchic social structure. Even to their own popular base, Communist regimes appeared to undercut Marxist ideology, thus allowing critics and their Cold War nemesis to claim moral superiority on the issue of "equality." All along, hierarchies at all levels of society East and West prevailed and the question was who is better off materially--Communist East or capitalist West? The thin layer of Communist regimes resting on top of a multi-layered hierarchical society was hardly sufficient to alter peoples' hierarchical values and envy of Western materialistic culture.
Since the French Revolution the proclaimed ideal of governments as often reflected in their written constitutions is egalitarianism in some form. Invariably this is translated into equality of opportunity in Western bourgeois regimes, a model exported to most of the world with globalization and the downfall of Communism. The (hierarchical) reality of course is far from the unreachable (egalitarian) ideal. While merit-based system is the aspired ideal of businesses, an ideal that business often projects as "equality of opportunity," the reality is one of rigid hierarchy often unrelated to merit-based models.
Given that educational and non-profit institutions have followed the business model, hierarchies prevail in those sectors despite the ideal of egalitarianism. Hierarchies may not only be the result of social conditioning, or inherent societal conflict where each individual struggles to maximize his benefit as Weber postulated, but they may have a psychosomatic basis as well. If we accept Jean Piaget's theory of cognitive development and Carl Jung's "stages of life" theory, then hierarchies are a reflection of human nature. Shaped by society's institutions invariably dominated primarily by social and political elites, human nature is conditioned to accept hierarchies as "natural." In the Middle Ages the Divine Chain of Being (the ultimate hierarchy) was reality throughout Christendom. Human beings thirst for affirmation of self and the desire to transcend self, they struggle to maximize their individual benefits oblivious to the welfare of the community. Therefore, they live in hierarchical structures because hierarchies are an expression of neurosis to use a Freudian interpretation.
However, at the ethical and socio-political levels, the elites and most people in Western societies acknowledge that some basic rights--human rights--must be conceded because we live in communities, share a common fate, and aspire to harmony that yields safety and security. At the existential level, death as the great equalizer representing the inevitability of eternal oblivion, the realization that the individual is indeed an organic part of nature's whole forces human beings to feel empathy in order to feel human and overcome fear of death, as in Leo Tolstoy's The Death of Ivan Ilyitch. Given that equality cannot exist in the absence of integration with the whole and given the individual resists integration into an amorphous mass where will and ambition are surrendered to the benefit of the "whole," hierarchies which are externally imposed will remain for eternity.