Scientific investigation could have revealed that our universe is full of meaning and purpose. It could have told us that we are at the centre of the entire cosmos - that everything literally revolves around us. It could have told us that, unique among the world's creations, humans are ensouled rational beings; that the entire universe is only a few thousand years old and on a scale comprehensible to the human mind; that our lives have an innate dignity and cosmic importance; that all life is directed towards goodness and cooperation; and that there is some universal order that humans would find emotionally satisfying and inherently appealling.
It could have told us that there's more to objects than mere assemblages of elementary particles and their properties and it could have told us that human concepts have a direct one-to-one connection with reality.
But science hasn't discovered any of that. What we've discovered instead is a universe about 13.7 billion years old, unimaginably vast, indifferent, inscrutable, and governed by laws that, while regular and intellectually satisfying, bear no resemblance to the ordered worlds one would expect from human religions. We've found that we're all living on the skin of a single planet, and only on some parts of that - we can't even live on the summit of Everest, let alone high up in the atmosphere or out in the depths of space.
Humans occupy the tiniest and most insignificant nook of the universe, and they are a short-lived, recent set of organisms, related to bed bugs, magpies, and other creatures subject to and created by selective pressures. Science has revealed no heavens or hells, nor any reason to believe in them. It hasn't provided any evidence whatsoever of afterlives, nor anything to human mental life beyond the workings of the nervous system. There are no souls or ghosts.
People like to pretend that science and religion don't come into conflict, or at least don't have to. It's hard to know what they mean by this. Certainly plenty of scientists are religious, but that's hardly surprising - humans are capable of holding mutually contradictory beliefs in their heads, and in any case, you don't really need to think about the moral and metaphysical implications of scientific work in order to do it competently.
The methods of science are not necessarily in conflict with religious beliefs, either; it's not necessary to laud faith and dogmatic belief in the absence of evidence in order to hold religious beliefs (although it helps). If all the world pointed in the direction of religious belief - if unbiased empirical observation and rational inference pointed towards a meaningful universe with a loving god as its cause - then one wouldn't need faith in order to be religious. Religious beliefs would result naturally from simply looking at the world. We don't live in a world like that, though.
The findings of scientific investigation
point towards a universe unimagined by any religion. The evidence from the world conflicts with religious beliefs of every sort, and there doesn't seem to
be any space left for the Christian god or anything similar to it. Rather than science being institutionally hostile to religion, or scientists being individually hostile to religion, or the methods of science being inherently inimical to it, it is the findings, the discoveries, the image of the world derived from scientific methods, that really conflict with it. We have to confront the world, now, knowing that it is meaningless.