kinda off topic but as an atheist myself im not offended but i dont quite know what to say if someone says i'll pray for you or i prayed for you, etc. its usually like "thanks, i guess" type thing. its awkward but thanks for caring basically. if someone knows im an atheist (like friends and stuff), i would prefer they not pray for me or if they do then dont tell me about it. if they dont know then its a different story, doesnt bother me at all. all in all its just kinda weird cuz to the christian they think theyre helping even though you dont want their "help" and to the atheist its like if you respected my religion (or in this case lack thereof), you wouldnt circumvent my beliefs like that.
I didn't really know what to say on that "issue". I'm an atheist who hears all the time "I'll pray for you". I usually just leave it alone and say "Thanks". People mean well and they think it is a good thing to say.