I do think Rand was being a bit more complex than that. The whole point of "Atlas" is: the heroes are failing to win because they insist on acting as though they were in an ideal fair world, but those who who accept the status quo and work to win inside it will end up burned worse, because the system is structured to corrupt and consume them - meanwhile our heroes escape with virtue intact. "Atlas" constructs a spread of parasitic, beaten, adapting, fair-but-accepting, and fair-and-renouncing characters to illustrate this. Rand is trying to say "a rationalist who understood the rules of the game would decide not to play".

Really, the fault with "Atlas" is that it posits an awful world-spanning System that in factual reality, just doesn't exist. And without that premise it's two inches of wasted paper.