When people say that they're "praying for you..."

[Citizen James]

I think JSojourner hit it right on the head.   It's all about context.

In a positive context it's no worse than being told that someone cares, or hopes things turn out alright, or sends 'good vibes'.  Hey - may the force be with you.  Can't hurt, so no problem.

In a negative, it's about the same as an explicative.  (I suppose people who use it that way could be considered to be using the Lord's name in vain).   I get that some from a local cultlike group which solicits funds right by the exit of various grocery store.  The phrase "no thanks" often gets responded to with a really sarcastic "God bless you".