The Whore of All the Earth had a recent post in which the author was told by a Christian friend, "You know, I've been praying for you." When I hear this sort of thing, I find that there are two ways I can view the situation: I can reinterpret the statement as something less stomach-turning, or I can get mad. I usually manage to do the former.
In the best case scenario, I decipher "I've been praying for you" as "I've been thinking about you." So interpreted, I can respond positively to such a statement as simply reflecting the speaker's positive intention. If the speaker does not know I am an atheist, I can hardly blame him or her for poor word choice.
Yes, I suppose that the original statement does suggest Christian privilege. And yes, the fact that prayer doesn't work means that the person is doing basically nothing to help matters. But I am generally convinced that the speaker is usually talking out of ignorance and not any ill intent. Of course, if he or she knows that I am an atheist and says this anyway, it becomes a bit more of an issue.
This brings me to the scenario in which I am most likely to get mad. If the speaker not only knows that I am an atheist but responds to my disclosure of atheism by telling me that they are praying for me, I consider that more than a little insulting and may respond in kind.
How about you? Are there circumstances when you would not be at all bothered by such a statement and others where you probably would be?