There have been a couple things in the news lately that have reminded me of this.
PZ's (pharyngula) problem with Catholics. Read some of the emails he's gotten here. How many people said they'd pray for him?
And today, there was this story on the Pope's take on the Anglican Church's allowing women bishops. You know he disapproves. He's said so.
"I'll pray for you" is an expression of disapproval, cloaked in feeling sorry for someone, that they haven't been shown the 'light' yet. And of course, who knows the right answer? I do! You poor sap.