I haven't read Waking Up by Sam Harris, but I have read other books by him (Lying and Free Will), they weren't too bad but I'm not a fan of his writing. So I think if he tried to explain something difficult, I can imagine that no going well. He had kind of a more, "just trust me now and read the references later" take on writing, than a trying to explain all the things approach, but it kept the books short. Also, many of the sources cited were available without paying, so maybe you could try reading the references, then you might have an easier time understanding what he's trying to get at.
Difficult books for me are ones where I don't like the style of writing, but I still feel compelled to finish reading them because I like the story. I read Moby Dick when I was fairly young, it took me several months, but I finished it. I liked the story, but it felt like it suffered from many tangents and overly described things that had little to do with the story. I like the story in the Song of Ice and Fire series by George R. R. Martin, but I find his style of writing to be extremely difficult to trudge through, it's like listening to someone with dementia teach history. But I liked the story, so I was able to force myself through the first three books. They were difficult.