"I'll pray for you."

What Christians (and apparently now, Muslims 130127) mean when they say, "I'll pray for you."

Here's my question to you, Mr. or Ms. Christian (or Abrahamic god-pusher of any sort); Why even bother telling me, an atheist, that you will pray for me? However you imagine that playing out, it is at best a misuse of communication, and at worst a product of coercion.

You're communicating dishonestly-

Mentioning it to me gets you nowhere with me. I can't imagine you don't already realise that I think prayer is a waste of time.
If you were really concerned for me, and thought that sending psychic messages to your imaginary sky ghost would help, then why don't you just do that, and not tell me you are going to do it? That would make much more sense, if indeed you actually believed such un-efforts would be efficacious. But why mention it? Because the weight of your intent is not actually on the prayer, is it? However silly that alone would be, you are just trying to shirk further discussion, when faced with cognitive dissonance.
You throw the phrase off like a lizard detaches its tail, and in some part of your mind, you may also realise the phrase is worthless in its literal sense.

You're just being selfish-

When you realise that you're being dishonest, you wish to mitigate your own self-judgment by hearing yourself saying what you believe to be righteous words.
'There, I said the nice *christian*(muslim) thing.. I'm good.. I'm not a liar for jesus (or Mo)."

You think you're being watched-

You're putting on a show for your imaginary judge. You've got to choose carefully from that limited superstitious phrase set, don't you? If you don't say the appropriate magic words, then it will show up as a negative tick on your heavenly credit score. Your god is watching you! Never mind the inconsistency that he's supposedly all-knowing in the first place, and would discern you're underlying, platitude encrusted motivations anyway.
But it doesn't end there! Who else is watching? Others of your "faith".
Despite what they say, they do judge, and you're afraid of that. You have to be careful not to say what you're really thinking, like "fuck off," lest your congregation cast a glance of disparagement your way.

So let's try just a bit harder to put an honest face on it, shall we? If you really and truly wish to pray for me, go ahead and clench your eyelids resolutely firm to your little delusional hearts content, dance a dance, make a grass doll, whatever. I just don't need to hear about it. And if you think I do, take a long hard think about these, your more probable motivations.