WAR is a zero-sum game so if Yadier Molina has value that isn't being properly attributed, that means his teammates (especially his pitchers) were actually worse than they appear. It also means that other MLB catchers were a lot worse than they appear.
Ivan Rodriguez has the top RField for catchers with 147. Do you think Molina saved 100 more runs than Pudge Rodriguez? The defensive rankings for catchers are: Rodriguez, Molina, Gary Carter, Bob Boone, Jim Sundberg. WAR seems to be doing a good job identifying the best defensive catchers. Are you saying all the good defensive catchers are underrated? That would mean WAR is not giving enough defensive value to various defensive events. Blocked pitches, caught stealing, wild pitches and fielding bunts are pretty easy to quantify the run value so that can't be where the error lies. It would have to be that credit for strikeouts and walks that should go to the catcher is instead going to the pitcher.
To be better than Mauer you have to believe that Molina has over 110 runs of defensive prevention that aren't accounted for. That would increase his RField from 138 to 250+ (while leaving Mauer's static even though he was a good defensive catcher). It would mean his pitchers got 1 WAR of extra credit that he deserved every season.