Please never ask, "Do you mind if I pray for you?" I can't tell you how offensive I find that, and how difficult I find to answer it without being offensive in return.
"I'll pray for you" is okay, I guess, but don't expect a thank-you.
I wrestle with such things. I am not religious -- I actually have a fair amount of baggage about religion but I try not to be an asshole about it (and, no, I am not suggesting you are being one -- I just know how contemptuous I can be). I have known way too many religious folks who seemed to be doing their darnedest to give religion a bad name, but I don't think it is fair or nice to then assume that all religious folks are of that ilk. I prefer it when someone is trying to respect my boundaries and not cram their beliefs down my throat, so I think I would be inclined to view the question as an attempt to respect my boundaries, yet would not be entirely comfortable with it either because "agreeing" to have them pray for me makes me partly responsible for their action when I don't really believe in it.
I currently live in The Bible Belt and I find that saying "bless you" or something similar when turning down favors is the best way to get rid of someone. IE I try to speak their language, even though when I use the word "god" in regards to my own beliefs, I am just using it as short-hand for "whatever intelligence there is behind the workings of the universe". That happens to be a mouthful and problematic in most social settings, so I often settle for "god" as a means to facilitate communication. In most cases, they aren't going to talk to me enough to ever have any real idea of what I believe so I don't see any reason to get all hung up about it. Still, I continue to wrestle with how to respect someone's beliefs and their good intentions towards me when there is often a vast gulf between our beliefs.
I don't have a good answer, just similar discomfort.
People expressing that they care in a way that, to them, makes sense is "presumptuous"?
Again: you can choose to accept kindness in the spirit in which it was intended, or you can be the Angry Atheist Asshole. The latter seems to be poor form.
"I'll pray for you" is okay, I guess, but don't expect a thank-you.