The term is problematic for many reasons (I assume we will get into those reasons, here), but it shouldn't be.
The term refers to a state of "notness," similar to the term "sober." It's the natural, an affected state. The default.
Sober, means "not drunk." Infants are sober, just like chickens and jellyfish, though we don't apply that term to infants, chicken, or jellyfish, unless there's extenuating circumstances that merit the term's use.
Atheist, means "not a god believer." Infants are atheist, just like chickens and jellyfish, though we don't apply that term to infants, chicken, or jellyfish, unless there's extenuating circumstances that merit the term's use.
Sober doesn't mean "good" or "law abiding," and plenty of horrible people eschew alcohol consumption. And atheist doesn't "bad" or "communist," and plenty of great individuals eschew God belief(s).
Why is there so much confusion over this term?