Look, I know you mean well. I know that no insult is intended. But try to look at this objectively:
Saying “I’ll pray for you” because I don’t believe in the same thing you believe in has the same affect on me as if you said, “I’ll ask My Little Pony to give you sweet dreams and chocolate.” It’s meaningless to me.
The reason it’s insulting is because what it really says is, “I pity you because you don’t share my beliefs, and therefore since I am superior to you, I will grant you this boon, you poor unfortunate soul. Thanks to me praying for you, you may escape an internal torment in Hell, you evil person. You should thank me.”
In other words, the only person such a statement serves in this context is you. While you mean well, it ignores my beliefs completely, telling me that you’re completely insensitive to them.
Someone saying “I’ll pray for you” as soon they find out I’m a non-believer is equivalent to me saying “I hope you get smarter” when someone tells me they do believe. It’s condescending and insulting to your belief, because it completely discounts it and treats it as meaningless and beneath respect.
I will gladly debate religion with anyone, but let’s not start off by insulting each other for our beliefs.
“I’ll pray for you” also depends on the context. If you’re saying that because I’m in the hospital, then I know it means “I am wishing you well” and I am happy to receive such thoughts. I take no offense, because it means you care. But when you say it in response to learning I don’t share your beliefs, it’s dismissive and insulting.