OK, I will try, given that I am mere a poor asshole.
The classic literature (and Atlas without any doubt belongs to so called modern classic) much like classical music, is a complex and highly artificial phenomena. The word for referring to a piece of art is artifact.
In the case of classical music there is absolutely no objective criteria to judge symphonies. It is possible to compare the pieces of music, and lots of pseudo-intellectual assholes do it for living, but it will be nothing but a joggling with a metaphorical jargon. Nevertheless, one almost always could distinguish some fragments from this or that piece of classical music which he likes for some not very articulable reasons. Bach, arguably, composed most of such sources of a beautiful fragments, Mozart is the second, etc.
These notions could be applied to literature. Like a symphony, a big novel, even a small poem, cannot be judged by a single criteria, but some parts of it we might find delightful and beautiful. The question, as it is in the case of classic music, is who is the reader (or listener).
In case of Atlas Shrugged, there are too many to count arguably beautiful parts (majoring in physics and philosophy is one of them), fragments or even passages, which appeals to the mind of modestly educated reader. The best personages she created were, ironically, not the central, heroic and positive, but all the crooks and weaklings, mediocrities and minor idiots. This, perhaps, is why Rand is hated so much.
As a student of philosophy, Rand got most of the philosophic and economic aspects right. Indeed, her Hegelian professor is a true masterpiece, her bureaucrats are convincing, James Taggard is remarkable. Her main characters are overloaded with virtues.)
Certain naivety of the plot - the miraculous alloy and especially the perpetuum mobile, for which the book has been criticized so often by idiots, actually are mere nuances. The real story is about focus and persistence, accepting the challenges, adapting and evolving and never giving up - all the postulates of a sound moral philosophy, which goes back to ancient Greeks. No one takes the plot of Atlas seriously.
She is also right that the motivations which drive us should be simple and pure (the Greeks, again), should be grounded in our human nature (shaped by evolution, constrained by biology) not in some abstract nonsense, dogmas, fleeting fashions, or even social norms. Rigid social norms are always reflect the ugliness of urban societies. While her main characters are rather angular and clumsy, the driving forces behind them are clearly recognizable and proper. Let's not blame Rand for this angularity.
I could do it for hours, but I think you got the idea. Good literature requires a "good" reader to be able to appreciate what is behind the words in a sentence.