I’m praying for you:
I had a guy say this to me last week who was not a fan of my work. And although sometimes people mean well when they say this, often times it’s basically the religious equivalent of the middle finger (I don’t like you and wish you would change, so I’m going to pray you become more like me). Now, there are those times when people say it with truly benevolent intent, but it’s still a very personal thing. Instead, consider asking someone if they would like for you to pray for them, and ask what they would like you to pray for instead of making too many assumptions.
That last line’s not a bad idea… because most atheists are just waiting to respond with “And I’m thinking for you.”