Next, the book was not meant to be just a story that entertains. She felt very strongly about certain ideals since she transitioned from Communism to Capitalism, and she writes at the very edge of the continuum. You read it, you analyze it, you adopt the ideals that make sense to you and reject those that don't. Not sure why this concept is so foreign nowadays. I don't share her atheism, but I certainly share her ideals on capitalism.
That may be very well for you, but Ayn would say that if you disagree with any of her ideas, especially including atheism, then you don't understand her at all.