This is one of Christian culture's very favorite things to say. Whether they actually will pray or not is anyone's guess, but it seems important somehow that you believe they will. Versatile and efficient, "I'm praying for you" can be used in absolutely any situation to cover several evangelical bases and tend to egos all at once. With just four words it's possible to establish yourself as spiritual alpha dog and signal an end to the conversation under the guise of bestowing blessing. Delicious and nutritious!
You may not find a less relational phrase in all of Christianese than "I'm praying for you." When said in response to an expression of pain or heartbreak it often shuts the conversation down. The person sharing can feel as if they've been stiff-armed and kept at a distance by the person they were confiding in so they can be passed off to God Almighty. The confidant can easily say this and remain detached, and if you've said it before yourself, it's that much more painful to hear.
People who are capable of casually informing people they're praying for them can't fathom that anyone could possibly have a problem with it. To their ears it's the most wonderful thing to say and anyone taking issue must be a jaded miscreant who's mad at God. (Anger at God is something else Christian culture does not endorse and does not deem permissible, but that's a whole other blog post.) This is a prominent characteristic of Christian culture: they have no idea how they come off. If anyone feels marginalized or dismissed by the allegation of impending prayer, the pray-er will likely interpret this as disdain for the whole of Christianity and take it as a cue to write that person off.
Saying "I'm praying for you" may be as relational as someone in Christian culture knows how to be. They're so busy Doing Things they may not know how to care and be cared for. All they may know is how to do is say things and remain detached, which definitely has its advantages. Actual relationship is a lot of work. Simpler to hold them at arm's length and avoid holding people's hurt than do the counter-intuitive work of bearing their burdens. When someone carries your struggle with you, the most healing form of relationship is taking place, and relationships are how we will all be healed. But they can be messy. It would be nice to keep this spirituality stuff within tidy boundaries. Which brings us to the hallmark of Christian culture: Doing Things and Avoiding Relationship. Keep this commandment and you will keep all the rest.
