It's true that you shouldn't just use the conglomerated CERA numbers of Salty vs. Varitek or Shoppach, you have to break it down by each pitcher.
But consider Lester and Buch for 2012:
Lester with Shoppach 3.70 48.2 innings
Lester with Salty 5.62 107.1 innings
Buch with Shoppach 3.23 78 innings
Buch with Salty 6.30 75.2 innings
As to the whys and wherefores of the problems with Salty, there are a lot of varying opinions on this. There was a report last year that the Red Sox brass did a sort of survey of the players on why the team's W-L record was so bad with Salty catching, and nobody seemed to have any clear ideas.
One thing to keep in mind is that all it takes is one or two pitches per game to have a huge effect on things. One pitch that goes the wrong way can result in multiple runs.
Another consideration is that Salty's performance might vary from game to game, inning to inning. Maybe he just loses focus sometimes.
Also, maybe the pitchers are aware of all these numbers and have less confidence when throwing to Salty.
There are a lot of possibilities, but in my opinion, the numbers over two years add up to Salty being a significant problem.