Is scientism such a bad word nowadays? Stephen Hawking, the great physicist, recently opened up his latest book titled "The Grand Design" with the sentence that, "philosophy is dead." While probably meant for effect and drawing off the idea that questions such as, "why is there something rather than nothing" is only speculation, claims such as these have given the impression that scientists are lacking in the philosophy department.
The favorite bugaboo for theists who are (somewhat) philosophically sophisticated is to point to problems in science. Most notably, the Problem of Induction and the Demarcation Problem. As you may be aware, the Problem of Induction just says that because, theoretically, every apple you have ever seen is red does not mean that all apples are red, as it may or may not be possible for apples to be different colors. The Demarcation Problem is probably the biggest issue in the philosophy of science camp and it deals with what constitutes science, how pseudoscience is defined, and what science can answer. And the latter portion of my simplified definition is the main point of contention coming from anti-scientnism types.
Obviously what is now referred to as scientism is an offshoot, or perhaps more accurately a direct descendant, of the logical positivism started in the Vienna Circle. The main idea was to apply the basic themes of the scientific method to the process of philosophy, eradicating most of metaphysics. As scientists though, I think this denies their place in history. During the enlightenment, the essence of a Renaissance Man was that he was skilled in many fields--primitive psychology perhaps, mathematics, language, epistemology, and more. Indeed, at that time, they were referred to as "natural philosophers" if their main preoccupation was dealing with the natural world.
However, I think the criticism of scientism mainly lies in the idea that it is nihilistic in nature. And by nihilistic, I only mean it to be value-free. It is, in its purest form, the strive for objectivity in a sense that is devoid of emotion and separated as best it can from the individual biases that plague our understanding of the world. While I actually believe this is an accurate depiction of science, I don't think it is an accurate depiction of those who claim that science is the best means to understand our natural world because the assumption is being made that they are mechanical robots. Obviously people such as Richard Dawkins, Stephen Hawking, and others who are accused of being scientism practioniers experience great emotion when doing what they love--studying the natural world. So I think it is strawmanning a bit to say that scientists are devoted in entirety to cold, harsh, objective reality and denying the more subjective and emotional experiences in life.
But there is no other way for the study of the natural world to be done. Seen this way, when a kid touches a hot stove and decides not to touch hot stoves from now on out, the kid is participating in some form of science, if you broaden the definition a little. Trial-and-error and pattern seeking is what we do best to make sense of our world. In a kind of Bayseian model, when new data enters, we adjust our theories accordingly. Perhaps the child in the example touched his first stove and it was hot, thus the idea that all stoves are not to be touched is created. If a stove is touched that is not hot, we may create a new theory that we should check to see somehow if a stove has been heated and maybe that will be a good model to determine the probability of it being too hot to handle. Basically, any concept we derive in the universe is a model of the reality that we are experiencing, and I believe it is pointless to pontificate on whether or not we can actually Know (with a capital K) or experience the "external world." We develop models that have explanatory power and serve us with predictive utility, and that is all science is aiming to accomplish. Science is in a constant state of discovery and updating, and the fact that it is not immutable is one of its greatest strengths, much to the contrary of theistic rebuttals.
Now, even with that said, there is a place for testing and a place for broader theory, which I consider a different type of science. If I'm allowed to interject a tad of political ideology, the economist F.A. Hayek, who was good friends with philosopher of science Karl Popper, was actually the one credited with popularizing the term, "scientism," and the criticism was not based on theological grounds. What Hayek was proposing was that, at least in the social sciences, people, and the interactions of people, are not as predictable as inanimate objects. What you have are minds studying other minds, so it is a difficult thing to do. Hayek's proposal was that you need some type of theoretical framework with which to draw practical conclusions or educated guesses and that equations and such are overrated in social sciences, and I tend to agree with that sentiment.
Another valid criticism of scientism I think is that for many it does eliminate practical concerns such as meaning and direction and even some political theory for that matter, at least when taken to its fullest extent. Because it relies so heavily on empiricism for the natural world and it is reductionist in nature, it has explanatory power for natural phenomenon but people who see the value in that tend to fall into the trap of denying emergent concepts. An emergent concept can be something like meaning or value that has an entirely naturalistic explanation but is best explained on a "philosophical" level, if you will.
If I rambled, I apologize but I believe scientism is an important topic. Nietzsche was right when he foresaw nihilism as a sweeping phenomenon. A scientistic mindset may isolate us from enjoying the more "irrational" aspects of life, such as art, beauty, and meaning. Now that may or may not be a bad thing, and it seems undesirable to me personally. Empiricism is not a bad thing when evaluating opposing claims about the nature of reality, but there is nothing wrong-headed about using philosophy/metaphysics to explain the material world's emergent properties. Theists have a mistaken view of scientists if they assume that those scientists believe science is the only means to reach any sort of understanding, although there are some of those people running around (Peter Atkins comes to mind). I believe it is not representative, that theist's ideas of nihilistic scientists are strawmans, and that admiration for science is a great thing.