Let’s assume someone, perhaps under the influence of LSD, believes he can fly–or perhaps (he believes) God has told him he can fly–and so he jumps off a building intending to fly away. But instead he falls to the ground and dies. The reason is that his belief was incorrect; it was counter-factual. It did not conform to reality, or at least to a certain subset of known physical reality.
Now I’m well aware that the notion of “fact” is a slippery thing and there are many kind of beliefs and worldviews and mindsets that do not fall as cleanly onto the spectrum of fact vs. fiction as the belief that you can fly. However, one can stipulate that not all propositions in the world are necessarily characterizable as provable facts without abandoning the claim that some facts, physical or otherwise, do in fact hold.
Like the acidhead falling tragically to his death, behaving in ways based on beliefs that are contrary to facts, no matter how strongly those beliefs might be held, is counterproductive and destructive. Such behavior is highly likely to reduce whatever metric you care to choose for quality of life in the broad sense. Of course, one can always adopt contorted positions such as claiming that some kind of satisfaction derived from the very fact of holding a possibly counter-factual belief–perhaps social approval from a group of like-minded believers–offsets the detrimental effect from counterproductive behaviors based on that belief. However, when taken to its extreme, this kind of logic would lead to bizarre claims such as that the person is better off lying lifeless on the ground because at least he had the satisfaction of holding on to his belief in this ability to fly during the last few seconds of his misguided life, and his widow and now fatherless children are also better off because at least he proved true to his beliefs.
People pushing this view of a false equivalence of science as just another religion trot out pretty much the entire litany of known types of logical errors. For instance, they might claim that people who believe in science are obviously deluded because they think that science can explain EVERYTHING, even though that is not generally true (although they may believe, correctly that it can clearly explain more and more over time). They would claim as proof of the equivalence the observable fact that scientists hold some unprovable beliefs, including perhaps even some about the scientific process itself. But no such arguments invalidate the basic notion that science is an endeavor which has successfully sought, continues to seek, and will continue to seek verifiable, useful, knowledge about our world, which will improve our lives by any common-sense metric. Interestingly, one of the areas in which science has sought such knowledge is about the question of why people believe in religion, with emerging results in fields ranging from evolutionary psychology to neuroscience. Perhaps the simplest refutation of a faux symmetry between science and religion is to note that while science tries to and is (slowly) succeeding at explaining religion, religion makes no attempt to and has not succeeded at explaining science.