Things by Palahniuk and Rand can have a ton of intellectual value. Anthem is a good story, and everything I've read by Palahnuik has been well written. They make you think, and even if you don't come to the same conclusions as the author wants you to, at least you can see how they got there.
I agree. If you judge a book by what you get out of it rather than what the author's ideas and motivations are you'll probably enjoy your reading a lot more.
That boils down to reading purely for pleasure, in which case fiction may be more effective. The whole point of non-fiction is that it should NOT be fiction, which requires intellectual honesty.
No, I think it boils doing to engaging with whatever you're reading rather than just consuming it. For non-fiction you can encounter the same facts as the author and reach different conclusions. Take something like Outliers, you can read it and say that his conclusions are too broad, but still get something out of the book.