It's a badly written book. Whether the ideas in it are nonsensical or not, the writing is terrible.
First, the book should have been about 500 pages rather than 1100. Atlas Shrugged's length was inflated by awkward descriptions and pretentious faux-literary writing.
Second, people read each others' minds too much in the book, and it gets really annoying. There are maybe hundreds of lines in the book like "he saw her three-fifths of a smile and immediately knew that she wanted him to meet her at 9:15 behind the statue of Henry Ford to exchange more facial expressions." Somehow, even though the main characters are basically high-functioning autistics and unable to relate to most of the people they interact with, they're better at reading body language and subtle lip-twitches than The Mentalist.
Third, the romance scenes are terrifying. Based on what she wrote in this book, the way Rand apparently views sex is terrifying. It's more difficult to describe than "sex is bad" or "sex is good," but it clashes with what any normal person has experienced. Anybody who has read this book can't really be surprised that in real life, Ayn Rand had creepy ideas about how sexy some famous serial killer was.
Fourth, there's actually a Reverse Robin Hood character who robs government transport ships and gives what he steals to the victimized rich people. He's one of the biggest heroes in the book. He also doesn't really fit into the philosophy of moral selfishness that Rand espouses, but that's another discussion.
Fifth, everybody who is good is tall and thin, and everybody who is bad has something physically unappealing about him. The bad guys are short, pudgy, ugly, hunched over, snakelike, ratlike, and in one case, a minor bad guy is too handsome in an apparently nauseating way. The good characters are all varying degrees of tall and slim, as I said. I liked keeping a height chart in my mind for all the good male characters (something like D'anconia > Rearden > Galt > Midas). A short person never surprises you and turns out to be intelligent and productive. I guess it's impressive that she managed to have so many characters in the story who were nearly identical in stature and personality (oh yeah, that's another problem with the writing).
Sixth, besides being short and fat and ugly, the bad guys in the book are just generally comically obvious straw men.
Seventh, the book is really boring. Getting through it is an excruciating experience. I think it took me about a year. Every page of the book was an effort for me, and I don't think I even once managed to read more than ten pages at a time after I was 100 or so pages into it. I'll never understand how there are people out there who actually say they enjoyed the book tremendously and read it in one weekend. There isn't enough of a plot to justify even a 500 page book. It's not compelling. The characters are boring and unlikable. Plus all the other things I mentioned.
Eighth, I almost forgot, there's a scene in which, right before collectivism causes a horrible accident, she justifies the death of every single person on a train because they donated to some cause or collected government assistance or were lazy or something. The one good, hard-working person on the train, a conductor, sneaks out the back with a sigh when he understands that the engineer is going to lead the train to its doom. The events of the book are so unrealistic and convenient to her philosophy that it makes it harder to take her philosophy seriously, while also causing the book to fail as a novel.