I don't want to say you missed the point, because that sounds rude. I do think Anathem is directed very, very specifically at people who already have a given nonfiction body of reading in their past. As an ... action novel, or an adventure story, or even as an entry point into modern philosophy, it misses the mark.
In the end, it's rather like Cryptonomicon, though. Smart people put into tricky situations and forced to solve them or die. My favorite genre.
EDIT: good that you finished it. It lends your criticism validity, at the very least.