Natural religion might have the following meanings:
A synonym for "natural theology"; religion based on reason and ordinary experience rather than supernatural revelation, although not necessarily denying it. This usage was popular in the 18th and 19th centuries— see, for example, David Hume's Dialogues Concerning Natural Religion.
In the modern study of religion it's used to refer to the notion that there is some sort of natural, spontaneous religious apprehension of the world common to all human beings.
As a reverent form of nature-worship, embodied in a well-known quote from Frank Lloyd Wright: "I believe in God, only I spell it Nature."