Worshipping/revering the natural universe, Nature, "reality", as it really is, does seem quite a rational stance. Albert Einstein wrote about the "cosmic religious feeling", which has nothing to do with a personal God.
Problems come when, as has been mentioned, the universe is viewed to have magical properties and/or moral properties in the absence of evidence. Then it becomes just another false deity.
There is a difference between naturalistic forms of pantheism and more superstitious ones. Philosophically though, the naturalist ones are not really that distinct from atheism.
Spinoza used "God" as a synonym of "Nature". That got him kicked out of the Jewish community for heresy. It's easy to see why this stance is antagonistic to belief in Yahweh. Spinoza may have been God-intoxicated but it wasn't with a religious deity, more with reverence for the natural order. There is no need to buy into Spinoza's antiquated views on metaphysics either to accept this point.
Then again, the term "God" carries a lot of baggage so may be best discarded. Even so, the distinction between the most naturalistic forms of pantheism, and full-blown atheism, is more a matter of semantics than anything else.