When someone says "I'll pray for you"

 

I get the reasoning and the mindset.

But at the same time, I don't think it's great.

If a believer within whichever-religion
says "I'll pray for you" to a fellow believer (within whichever religion),
that's fine.

But when they say it to a nonbeliever,
in regards to:
trying to cure a person's non-belief (or allegedly wrong beliefs),
then it's like a Jehovah's Witness saying that to a Catholic,
or a Catholic saying that to a Baptist,
or a Wiccan saying that to any "Christian",
etc..

It's only going to come across as passive aggressive, self-righteous posturing
from "a praying person" who (as far as the other person is concerned) is in a creepy cult.

They are also going to immediately realize (unless they're slow) that the compliment of "I care" is mixed with an equal amount of insulting "you need to be more like me".

There are plenty of people in this world who I am really really sure would be a better person if they were as thoughtful, compassionate, and personally accountable as me.

It's perfectly fine for me to realize that; about myself and about them.
But if I ever actually tell them so, it would only further polarizing them against me
and move them further away from that path.

At the same time, I realize there are plenty of people in this world who have strong traits that I wish I had.

In those regards,
if I became more like them,
I would be a better person.
 Or, at least, a healthier person. 

However, when it comes to religious prayer as the premise for such an expressed sentiment,
that's actually worse.

It would be like a literalist Satanist saying "I'll perform a ritual blood-magic incantation tonight, to make sure the Being I worship pays you a visit. To straighten you out. You know ... because I care".

It's better to not even let the other person know.
It's not as-if a "God" only grants wishes if you let the other person know you're going to make a prayer-wish about them.

Besides, what is a "God" going to do anyways?
Make them want something they didn't already want?
Make them feel something they weren't already trying to feel?
Maybe implant a thought into their head they didn't choose to have?

The only way for a "God" to avoid messing with their "Free will" and still influence them "towards Him" is to: 1. materialize like Morgan Freeman in "Bruce Almighty", 2. have a heart-to-heart conversation, and 3. do some personal miracles to meet that person's standard of evidence.

Anything else would be a violation of autonomy.

Plus, every time you tell "God" something, or give God some advice in the form of a "humble request", ... "God" isn't slow. He's going to immediately recognize that such prayers are NOT an act of faith. They are an act of doubt. Because it means you weren't sure he noticed enough, or weren't sure he cared enough, or weren't sure he realized the best course of action in the moment. And so you were 'there for Him', to help clue him in to what he aught be noticing and aught be doing.