Even as a Christian, I often find this phrase offensive if uninvited – especially so if there is some sort of disagreement involved. It seems to me to be just a passive-aggressive way of saying, “I’m telling God on you”.
Telling someone you know doesn’t share your particular beliefs that you will pray for them is probably the ultimate condescension. It indicates that you believe you are morally/ethically/spiritually superior to them and have a special hotline to God they could only wish for. It gives the superficial sense that you are taking the moral high ground, when in reality you are hitting below the belt.
And when used in a disagreement, consider what you are basically going to petition God for anyway… that the person you disagree with come around to your way of thinking? Now isn’t that just the height of hubris?
I once heard an atheist say that a Christian telling him, “I will pray for you” is just as rudely obnoxious as him telling the Christian, “I will think for you”. It’s like throwing meat all over a vegetarian’s salad.
Don’t get me wrong, It is perfectly acceptable to pray for people, especially your “enemies” – but do so privately just as Jesus instructed [Matthew 6:5-6]