The answer above explains the core of fatalism in the novel and how it explains the paths of the protagonists. The modern reader might struggle to understand why the protagonists do not simply move to a distant town and tell nobody of who they are, but their consciences and Christian values prevent this: they are sure they will be found out.

An excellent example of naturalism at work in the novel can be found in the tragic tale of Little Father Time. A child of Jude, he literally enacts natural selection by killing himself and his siblings "because we are too menny." In an attempt to reduce the difficulties faced by his parents, he eradicates himself and his siblings, his childish misspellings highlighting his youth. In Little Father Time, we see a painful example of Darwinism as cynicism in this novel, suggesting that only very few could survive in the conditions of Victorian England.

Naturalism in the novel is almost a secular version of religious fatalism, in that it presumes that people are controlled by inexorable external forces rather than being free agents capable of self-determination. In Hardy's period, this notion appears in three forms. In Marx, one sees human action as determined by economic factors and social class. In Freud, the subconscious acts as a controlling force that manipulates the individual but that the individual does not fully grasp or control. In Darwin, we are all tools of the impersonal forces of evolution, driven by a need to propagate our species.

Jude exemplifies the protagonist of a naturalistic novel in the way he is trapped by external circumstances. Although he longs to follow the path of his teacher and pursue and education at Christminster, his intellectual and spiritual yearnings are overcome by his carnal nature. He is tied to his class origins and environment both by external constraints and his own sexual and reproductive urges. 

Jude and Sue also represent the problems of the Church of England in the wake of Darwin. As the literal reading of the Mosaic account of the origin of humanity was overthrown by Darwin and Higher Criticism, many people fell into spiritual turmoil, finding it necessary to reject either science or religion; only gradually did the Church settle into accepting the Old Testament as a figurative rather than literal account of Creation.