The cause of the fall of theism from the elite in Western society preceded the theory of natural selection (see here). What was the cause, then? In part, it was the introduction of a new system of truth, that could potentially conflict with (or corroborate) the truth claims of an extant system (i.e., various forms of Christianity, folk traditions, and so on).
Yet, the notion of truth is not static through this process. The introduction of scientific truth changed what ‘truth’ was – i.e., it’s ontology changed the notion of what could be ‘real’. This has led to contemporary academic philosophers, such as Daniel Dennett, denying that there is such a thing as subjective experience. Science trades in abstract, quantitative ‘things’ which are left as such. So, the logic Dennett might employ goes, therefore subjective experience is a mere illusion – it does not exist.
Yet, this leads to cognitive dissonance – the apparent fact of subjective experience is constantly before one. It is fairly straightforward to see that scientific representation is representation, which is symbolic, and so must be a symbol of something. Someone like Dennett posits the abstract symbols of science’s ontology to be transparently understood things in some relevant sense. So a response can be made: deny ‘transparent understanding’ vis a vis science’s things. If subjective experience is real and science is comprehensive in the relevant sense, then the symbols employed in science must be a representation of subjective experience at some point. So, in order to pursue this intuition of ‘facts’ and ‘reality’, one can say that Dennett posits an understanding of scientific things that is not actually obtained.
(One cannot say that subjective experience is not real just because current scientific ontology does not allow for it be real, say. Physical science has consistently expanded or modified its ontology upon discovery or investigation of phenomena with robust evidentiary bases.)