The natural world is the natural world. We all have access to it through our senses and we can all use its resources for our own purposes. What religion promises (often, but not always) is that there is an aspect to the natural world that is beyond our senses and our ability to understand.
Science can be said to do this too, but the difference is that science makes those hidden aspects available to all of us and tells us how we can access them too. Religion does not do this.
For the most part, religion — led by religious teachers and guided by holy books — asks us to take things on faith. It tells us to believe that justice will be done, believe that there are higher powers who care about us, believe that the guilty will suffer and the virtuous will be rewarded. Religion asks us to believe all these things and more. Some of these beliefs may seem harmless. Some may even seem uplifting and empowering. But the damage that they do is to our way of thinking.
When you believe in an aspect of reality that is imperceptible and beyond your ability to see at all, what is to stop someone from coming along and stuffing all manner of nonsense into that aspect? So the space that god occupies can also be occupied by telepathy, astrology, the afterlife, mystical powers, faith healing, and even claims about what you are required to do by orders of divine authorities.
What religion has done to our understanding of the natural world therefore is twofold. Human beings need to know, and in ages past, when we didn’t know much, it saved us from the madness of not knowing. It allowed us to live inside a framework of made-up answers about the natural world. It gave us the comfort of thinking that the natural world was made for us and we were allowed to use it for our benefit.
More recently however, religion has done little more than muddle our understanding of the natural world. The framework that once protected us from madness, is now suffocating us because we have outgrown it. We understand the natural world better than we did before, but our religious understanding of it is preventing us from accepting this newfound understanding completely.