I tend to be amused. If they want to waste their time doing something totally ineffective for me, then that is their choice. The only beneficial effect of prayer is a soothing effect on the psyche of the one doing the praying, which observation has been found repeatedly in studies in psychology. In other words, the only people they are helping is themselves! (smirk)
It depends on the context because with some you just know that it is meant in a condescending manner. My argument has always been if you are going to pray you only need one. “I wish the best of things for all things”. Cuts out all the strange prescriptions and personality-centric focus and, if it works, everything gets the benefit. Seems simple to me, but then I am a simple bear with little brain!
I think many Christians say this and don't actually pray. I think it's often something said to wish you well like Renickulous said. Sometimes people don't know what to say and it's they're way of saying I support you and want things to be better for you. If they do pray, what's it hurt? They obviously want good or positive things for you or want a situation to change. Sometimes people don't know what to say or do in certain situation, but I think overall these words have good intent and it isn't meant to push their beliefs on you.
Try not to be irritated. It is there way of doing something that may make them feel good, is that so bad? Does it affect you in any real way? I think we need to be able to love mankind regardless of beliefs. Except that someone is concerned about you regardless of the reason. It doesn't harm anything. But being defensive etc may only instill the belief in them that we are bad, evil, wrongdoers. Let them see the truth.
Besides, if you get if you loose your cool every time somebody says "I'll pray for you", you look like a douche and see people like us as just bitter. They win and you loose. Next time just say "no thanks" and/or "don't waste your prayers on me, pray for something relevant like a cure for cancer or something" see how their eyes gloss over.
Just ignore it. "I'll pray for you" is just their defensive mechanism and just as irrelevant as "bless you" whenever you sneeze. It's a cultural thing and with every generation there is less and less of this BS getting passed on. Be patient, don't loose your cool. Stay focused on the more important things like how laws are passed on use your right to vote.
First, what qualifies anyone to pray for you? Second, it's usually for some reason that is pretty petty in the grand scheme of things...like, you have the flue, or lost your wallet with all the cash you have....and this "god", who governs an infinite universe, has nothing better to do than to cure your cold or help get your sorry ass out of your financial bind! Talk about the hight of grandiosity!
I usually state, when someone tries to get me to agree in the powers of prayer, that "nothing fails quite like prayer". Then I suggest that a tangible act might be more effective (like loaning me 5 till I find wallet!)