Just words,
If you were to us F*** (rhymes with duck), that does not mean you are inferring its original meaning "Fornication Under Consent of the King", its just a swear word. To use god, christ, holy, etc, also has no inference other than its what we collectively say when people sneeze, we hit our thumb with a hammer or witness something unusual.
The phrase "touch wood" comes from a pagan ritual of tree worship, later as with many pagan rituals it was adapted to infer you were knocking on the wood of a crucifixion cross. Christianity has hi-jacked many pagan rituals and made them their own. So when someone says happy christmas to me I usually respond with happy winter solstice to you too.
Many phrases/rituals are derive from pagan traditions (pre-christianity) the word holy is only found in the English translation of the bible and again points to tree worship "holy tree".
Easter is another good example, named after a Saxon deity called "Eostra" and that was derived from a ancient word for spring.
So they are just words and I would suggest if an atheist gets upset with these words, it is by what is inferred by who is speaking them. If I sneeze and someone says "god bless you" I take it as just a thing that is said when we sneeze. However if those words are spoken to me when I have not sneezed then the inference has a religious meaning and I would take issue with the person, probably by sarcastically asking which "god"....
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