Oooooh…I get it. It’s the atheist version of that “Hate the sin, love the sinner” thing. Caughtcha! How progressive!
The difference is that “Love the sinner, hate the sin” is usually referring to homosexuality. In that case, the ‘sin’ is a part of who they are, and something they can’t change. Religion is a belief, that can indeed be changed.
“Your sexuality is inherently sinful and wrong, but it doesn’t change my opinion of you as a person.”
vs
“I hate Christianity, but it doesn’t change my opinion of you as a person.”
People’s religion is often as important to them (if not more so) than their sexuality.