When someone says "I'll pray for you", there are two possibilities. One is that you're sick or something, and a caring person wants to pray for you. This is wonderful, and I would fully accept the prayers. The second, and much more common possibility, as that "I'll pray for you" essentially equates to "you're a lost cause/evil/stupid/etc and only god can help you". There's nothing friendly about that.
I can't say I've ever had anyone use this supposedly "common" possibility, nor can I think of anyone I know who has.