Ok I as an atheist living in a very Christian country hear that. Especially around Christmas, Easter time, etc. But also on other occasions like helping an old lady crossing the street (yes there are still people out there, doing that).
Many atheists react almost allergic to "God bless you" or "I will pray for you"
There are certain points I would like to address on this matter:
1. Some of the people actually really mean what they say. They are thankful or want to simply wish you something nice. They say it with a smile on their faces and a glow in their eyes. Yes, they mean it. They believe in God and in prayer and they know that what they just said is something very nice. They assume that you are believing what they believe and that you find it very nice to be told something like that.
2. Some people use it as a "f*** you". That's often in situations when they know they can't argue, or they are annoyed, sad, etc. And a line like "I am sorry you can't understand my point of view. I will pray for you" Meaning "I hope you will understand soon but for now I am not open to discuss more!" or in short "leave me the f*** alone!" will be very annoying to you but grow up, get over it. Taking it as offence is only stressful for you and not helping or changing anything.
I made a few observations and found out some stuff when it is about "God bless you" and so on.
I do not believe and I don't have to agree on the religion but nice people who want to tell you something nice around Christmas time they want you to say something nice back. They say "Merry Christmas" and (by now) I respond the same way. I smile and say, "Thanks, you too" and then I close the door and live my atheist life. Saying it won't kill me, I do not have to go to church on Sunday mornings, when sane people sleep. I will not tell them "I will pray for you" and I will not be the first in the conversation who says "Happy Thanksgiving" but I will respond nicely.
I also know that many atheist are so allergic to it because they don't really understand something important. It is not simple ignorance that makes those people say that. They are brought up in a system where you get to think very religious, where you know that people around you either think your way or will think your way soon if you work on them. Their religious behaviour also has a way of talking in it. Wishes like "God bless you" and "I will pray for you" are so deeply stuck in them that you will not get it out of them, especially not if you react totally pissed.
Any of you atheists out there who tells me that a "thanks god!" or something similar never slips out of there mouth sometimes is a liar. Sorry to say that.
Yes religion is so hard to get out of you and me.
Don't blame those who are still brainwashed for your unhappiness that it is still not completely out of you....
Cheers and 'till next time