Scattered excerpts from one cranky dude:
Try not to take too much offense at this honesty, but the bare fact is that when you say, “I’ll pray for you,” I, as an atheist, don’t believe in God, so I see it as you talking to yourself. As a result, from my viewpoint what you’re telling me is, “I’m going to go talk to myself about you.”
When you say, “I’ll pray for you,” you seem to be (and, I would argue, actually are) trying to say that you’re superior to me. Now, atheists don’t believe in God, but when someone is unduly arrogant towards us, we become as angry as the next person.
A lot of atheists may appreciate the phrase when you use as they’re going through a hard time — but some atheists won’t, and they have a fairly upstanding reason for why: We atheists simply don’t think prayer really does anything.
Many of us atheists are familiar with Christianity, so we know that Jesus said to keep your prayers to yourself in several places in the Bible. So, we figure, if you sincerely wanted to pray for us, there was no need to tell us.
If you have no strong reason to back up your statements in an argument, “I’ll pray for you” seems like a cheap trick to psychologically intimidate the atheist into either feeling inferior to you or into feeling he or she is in a position of shame or pity, or to otherwise emotionally manipulate the atheist into coming closer to your position.
In any event, the growth of the non-religious and the gradual shrinking of fundamentalism seems to be making the phrase “I’ll pray for you” in an inappropriate context increasingly unacceptable.
Whatever. I don’t think I would even want to make your acquaintance. You seem to be talking about Christians (or maybe Jews) only.
You might want to be a little less combative if a Muslim says he will pray for you. Especially if you are in Saudi Arabia, where you are now classified as a terrorist.