I really enjoyed the historical context of Tom's response, & I imagine that those initial impressions are still a factor today.
For me, personally, I think it is difficult because it plays longer than the yardage due to the uphill nature of many of the approach shots along with the fact that it usually seems to play soft. Also, it has relatively skinny fairways and there usually isn't a lot of room to miss -- the end result being a lot of holes that have a penal / target golf feel to them. I first played the course in 2010 in the Callaway Invitational. Our playing partner for our rounds there was John Douma, a journeyman pro who never missed fairways (literally), averaged 285+ off the tee, had a great short game, and was a good putter. In the tournament round, I think he scraped together a 72 or 73. The rest of us, well.........
I came away from the course really disliking what I saw. My overall impression is that it was a waste of a great piece of land. Imagine if C&C or Doak had received that commission? The course would be a strategic masterpiece full of half par holes...many that are "gettable" and others that just kick your ass. There's very little of that at Spyglass. The overall sensation for me was a slog with a terrible stretch of finishing holes. In sum, a missed opportunity....
I compare that experience to the one that I was fortunate to have this year at Cal Club. To me, Cal Club is the antithesis of Spyglass. It's firm, fast, strategic, & full of holes that you can score on (or rack up big numbers on if you don't hit your shots). On every approach & recovery, I was trying to create a shot or play a bounce...a feeling that was basically nonexistent at Spyglass. On top of that, I walked 18 holes in 2.5 hours....At Spyglass, on the other hand, you find yourself gritting your teeth while you look for positives to justify the exorbitant green fee. Bottom line - it's a slog & it wears you out...this, more than anything, contributes to that perception.