What Rand says is more like "An awesome rationalist who understood the sick twisted rules of the game would leave and start their own game and not stick with those awful losers who make the world suck."

So sure, Atlas explicitly encourages embracing the reality of an unfair world full of parasites - the heroes' character progression comes through that acceptance. But the characters of Atlas implicitly encourage whining and bitterness, which are symptoms of failing to accept the reality of an unfair world.

And I think the implicit message affects readers much more strongly.