Every protagonist in Atlas Shrugged is without flaw. Each one is a genius in his particular field of expertise, and each one has a rigid moral code that won't allow him to take so much as 50 cents from the till in order to buy a quick soda. They are all paragons of virtue, übermenschen without equal, and if we would just let those people steer the world, then truly we would live in a utopia.
Now, where are all those people? Where are the men and women who are gifted with genius and drive but unburdened with any unseemly characteristics? In Atlas Shrugged every good tycoon voluntarily pays his workers well, ensures that their workplace is safe, isn't a racist, a sexist, a homophobe, or ever takes advantage of his employees sexually. They do this because it guarantees a good performance and loyalty, which is true, but we've all worked a job where managers and supervisors abused their power over us unfairly for their own gain. Not all of those were bad bosses or businessmen, not even most of them, but that gray area exists.
We're not saying that there are no people out there who are basically Jesus with a briefcase full of a new operating system, we're just saying that we haven't met them and they aren't on TV. Which is why you should always remember that...
That's all it is. It's a sci-fi novel with an agenda, but in the end it is simply a story, and that's why we enjoy it so much. We think the story is great, but let's not call it the operating manual of life.
Remember, Atlas Shrugged is a world almost totally devoid of loving families, of children, of any kind of positive religious faith, of soldiers who are anything other than hired thugs, and of any statesmen. It's a world where Eddie Willers, the only protagonist who lacks brilliance but still shows an iron loyalty and work ethic, is left to die in the desert while the rest end up ruling the world. In short, it's not the world we live in or really a world we would want to live in.
The lessons to take from Atlas Shrugged are that production is one of man's greatest gifts to mankind, to never give someone something that they don't earn or deserve, and that you should never let someone tell you a truth you know from your own cognizance is a lie. The lesson is not, "Turn over all control to private enterprise" or "The government is evil," it's to be a real, living, thinking person in all areas of your existence. Don't take our word for it, read the book yourself, and maybe you'll see that those who would use it as a lever to move the world to their benefit at the expense of yours are not necessarily its most orthodox followers after all.