"I'll pray for you."

Deema • nerd
Sorry to those of you tired of religious conversations, but I would truly like to understand the use of "I'll pray for you" or "You'll be in my prayers."
I think it's often used to console someone going through a tough time and let them know that you wish good things for them. However, I also feel like it is sometimes (often?) used in negative ways, as well. For instance, I've seen "I'll pray for you" used to dismiss disagreements or as a way to imply "Shame on you." 
So, for the *poll*, tell me how you use this phrase? 
As a follow-up, how do you feel about it being used in an insulting and/or dismissive connotation? If prayer is holy and sacred to you, why use it in a statement intended to insult someone?
Let's stay polite. :)

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