Most of the existing answers and many comments speak about how "materialism" is outdated and that "matter" is not underlying reality, since we know about quantum theory and field theory. I feel that this misses completely what OP is asking. OP is not asking about whether the universe is made from "matter" or "quantum fields", but asks about idealism, dualism ("souls") and so on and forth.
As explained in Materialism:
According to philosophical materialism, mind and consciousness are by-products or epiphenomena of material processes (such as the biochemistry of the human brain and nervous system), without which they cannot exist. Materialism directly contrasts with idealism, according to which consciousness is the fundamental substance of nature.
Materialism is closely related to physicalism—the view that all that exists is ultimately physical.
Assuming this is what OP is talking about, here is my answer:
To make scientific progress, it is irrelevant whether the universe consists of physical aspects only, or whether there is something "more" which lies completely outside of physical reality. It does not matter if there really are souls, gods, multiverses, fairies, or anything else.
Also, if the latter exist, science will never be a threat to them.
Science "is a rigorous, systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the world." At the end of the day, there are these logical possibilities:
- Either the "world" (i.e. the universe, reality, or whatever you want to call it) consists of only physical things - be it matter (which is indeed an outdated concept if you go down to quantum levels, but still an absolutely valid abstraction when we talk about the rest, which surely is still 99.99999% of science), quantum fields or even deeper concepts which we might find in the future when we solve the unification of quantum and relativity,
- or there is something outside of reality, like souls, gods which live outside of time and space, consciousness which is not caused by our brain chemistry and whatever supernatural phenomena you could imagine.
In the first case, there is no discussion to be had. Science is possible and there is nothing more to it.
In the second case, it will still be true that the purely natural aspects do indeed exist, for some definition of "exist". Science will always be the proper tool to learn about these aspects. The science of fluid mechanics will never depend on whether souls exist.
The only interesting question then remains: will science proper ever be able to be applied to these supernatural aspects? I.e., assuming that at some point in time we actually do figure out (or become convinced...) that something supernatural actually is true beyond any doubt, will we then ever be able to rigorously and systematically build and organize knowledge about said supernatural phenomenon. If so, then science will be enough to describe everything including supernatural phenomena. If no, then no.
But even then, science will still be applicable to all the rest, at least on the level of abstraction that we have today.
At the end of the day, this chain of arguments has been around a long, long time. Before we (re)started science in the west, in the dark middle ages, God was considered real and doing science brought you into bodily danger. Over time this shifted ever more, and ever larger swaths of reality moved from religion to science. It was always the case that some people would attribute features of reality that were not yet explainable by science would be attributed to God, and it was always the case that this realm got ever smaller and smaller as science improved.
Not once, ever, has anything at all ever been truly scientific and then reverted back to being outside of science and in the realm of Gods and spirits. Obviously many scientific theories and discoveries have been falsified, which is the very foundation (or even definition) of science. So not everything that science has ever brought up is true, but it is still scientific.
TLDR: So no matter whether it is God or some kind of soul or some supernatural basis for conscience; science will always encroach on it, there has never been even the tiniest, slightest hint (in science) that anything not open to the scientific process must exist. And it will lead to endless frustration for someone to insist that something supernatural does in fact exist in the "gaps" between the scientific know-how. It is, instead, very fine to just say that we simply don't know some things yet, or may not know them ever. There is no fundamental reason to pose that there is anything fundamentally different from physical reality.