I don't think they meant that the WRs literally don't know what routes to run. It's that they run them so poorly, Tony "doesn't know where they're going to be".
And IMO a lot of it is also what IR said -- the adjustments they make on the fly.
But Owens has always been a poor route runner. Look at how many of his big plays come when Tony buys extra time -- because that's a time when freelancing actually works.
Again, as IR said, Sham said Owens is a great athlete but could be a lot better (I believe Sham actually said terrible) as a professional wide receiver -- meaning precise routes, proper timing, and sure hands.
What's really troubling is how observers like Laufenberg see this, people inside the organization see this, but Jerry either doesn't know it or, much more likely, simply ignores it.