I think the notion of over or underrated is difficult to discern because opinions of his work can be quite polarized. His name still carries enough perceived weight that many courses go out of their way to market their connection to him, and he still has more name recognition among rank and file golfers than many other (more respected, here) architects. So in those circles I’d say he’s quite overrated.
Among an audience like this site, the opposite is probably true. Here, he is more synonymous with banal, dictatorial, golf courses that epitomize the “dark age” of design. Personally, I’ve only played around ten of his courses and I find them to be repetitive in design, particularly around bunkering schemes, use of water (over the water approach, anyone?), and tees (of course). I’ve played holes at Lido that were essentially the same as something at Hominy Hill, which were not unlike something I saw at Port Royal. That said, a course like Port Royal is a blast to play and is a very good golf course, but how much of that is attributable to the land and setting and not the architect? The holes on the lower, flat portion are uninspired and can literally be found at his other courses all around the world.
Are courses like Hominy Hill or Lido bad courses? Not at all; Lido has its moments and Hominy Hill is pretty solid, and that is what I’ve found in most of his work. Personally, I haven’t played an RTJ course that I would consider to be bad, but I haven’t played anything other than Port Royal that I would elevate, even to the level of “very good," either.