I can’t speak for all atheists (we’re as different and individualistic as religious people), but I can say that this atheist doesn’t get upset if you say “I’ll pray for you.”
I can see why some might find this upsetting. It’s a four-word rejection of all we believe in (or, rather, don’t believe in). “I’ll pray for you” can be interpreted as “I’m not going to even consider that you might be right; rather I’ll outright reject your world-view and hope that you’ll see the truth.”
I don’t quite interpret it that way, and even if I did, I see it as proof of chinks in the armor. I think nearly all religious people have doubts, and if they throw up the shields that quickly, they’re trying to hide those doubts.
But I see the whole “I’ll pray for you” thing differently. Probably because I’ve heard it from some really great people, those who have conversed with me about non-belief and tried to make some effort to understand it.
I have one religious colleague in particular who I know is genuinely concerned for my soul. He is a devout Christian and believes that those who do not accept Jesus as their savior will suffer in Hell for all eternity.
I admire his courage and honesty. I find a lot of Christians I’ve talked to have a really hard time facing up to what the Bible teaches about this, that people they know and like, perfectly good people who happen to be Jews or Atheists or Muslims or whatever, are doomed to Hell because they don’t buy the story. It’s one thing to consider this in the abstract; it’s another to consider that the person sitting next to you—specifically me—someone you regard as a friend and know to be a pretty decent and caring sort of person—is destined to suffer for all eternity. It makes them very uncomfortable. (Don’t blame me, I didn’t write the book.)
So my colleague is genuinely concerned that I won’t join him in heaven, and he prays for me. Others I know have expressed similar sentiments.
I see this as the ultimate compliment. To me, “I’ll pray for you” in this context means “Listen, I’m going to devote part of my time talking to the most important guy in the universe, the one who controls everything, and ask him to intervene on your behalf.” Is there any greater expression of love from someone who truly believes?
So I don’t get insulted when people say they are praying for me. I think it’s a rather nice thing to do.
I think their prayers are unlikely to have any effect, and not just because I’m a natural-born contrarian. Emma Ryan, who ran the Ex Scientologist Message Board, used to say “Some things, once seen, can’t be un-seen.” I’ve come to the realization, to paraphrase Julia Sweeney, that the world works exactly the way you’d expect it to if there is no god. It’s impossible to envision me transitioning (or, perhaps I should say, returning) to believing in something I know to be so highly, highly improbable.
Also, I don’t think anyone’s listening to those prayers. At least, no one in a position of universal authority.
Still, it’s the thought that counts!