Does it matter? Isn't the point to read these ideas and to as with all good ideas they get told in many forms. As with art movements, perspective shifts and whole genres of the arts move in unison, from performing arts to fine art. Unless as is the case with some ideas, the medium is the message, then the format used, be it a nice comfortable paperback or a think hardcover text is of no importance.
Does it matter? Hmm. That's a good point -- it may not.
But ZAMM and Atlas Shrugged certainly felt to me a bit dishonest in that these works are primarily delivery devices for the authors' philosophical ideas. Other authors inject philosophy and ethics into their "straight" fiction, such as the philosophical rant-free work of Tolkien (LOTR = a treatise against fascism) and Stephen King (The Stand = a treatise against organized religion), but their philosophies never smack you in the face. [edit: grammar]
I think it's okay to smack the reader in the face with all sorts of knowledge provided you're sufficiently up-front about it, make sure there's more to the book than that, and give the other side a fair voice. (MoR!Dumbledore, MoR!Quirrell, the Lady 3rd Kiritsugu from Three Worlds Collide...)
I suspect that what goes wrong is not writing a philosophical treatise in the form of fiction - what goes wrong is that the One True Philosophy is treated as a Mary Sue within the context of the fiction.
