Clearly you are welcome to do whatever you please in your own head, but telling someone whom you don't know well enough to know that they share your religious beliefs that you will pray for them as a way to show your displeasure with their life or a decision they have made is condescending, and rude.
My wife, my daughter and I went to the store:
Lady at the store, speaking to my daughter: "Aww your dress is so cute"
Daughter: "Thak you. My auntie bought it for me"
Lady: "Oh how nice, is this your auntie?" (gesturing to me)
Daughter "No this is my mom"
Lady "Oh, well is this your auntie" (gesturing to my wife)
Daughter "No, thats my mom too."
Lady "Oh my. Im going to pray for you all"
Me: "Please dont!"
Its not cute, it's not polite and your kidding yourself and everyone else if you actually believe that you are being nice or genuine when you say it.
If you are going to be so rude and imposing as to hide behind religion to be a hateful twat don't get upset about people being rude back to you when your 'prayers' are not appreciated.