Another reason that people sometimes use the word "universe" -- in addition to the things already mentioned here -- is that God often has the connotation of a transcendent being. In other words, God is something (usually a being) outside of humanity, different and other from nature, which is beyond experience, and exists apart from the physical universe. The Universe is often described as being immanent -- that is, permanently pervading and existing in the physical world, sustaining it and operating inherently from within it. God is also generally conceived of being a singular entity, a being, without plurality, but in some sense definable, if only by saying what God is not. It's hard to define the Universe in terms of what it's not, and it's not so much thought of as a singular entity, nor as a being.
A term I have heard suggested as an alternative to these which (theoretically) embraces both the immanent and transcendent views is "The Ultimate" ... but I'm not sure if I like that any better or worse.
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