I think issues like politics can and do play a roll - although how much they know about J&D's politics is another question (c.f. the discussion on the Folk n Roll thread, about whether Universal Coward is actually a pro-War song, or a satire).
There is also the issue of how general attitudes to J&D have developed over the years. They are simply - in Europe at least - not a "cool" band. Those who have heard of them (which is not many over here) associate them with the BBs (also not a cool band), and the generally maligned music of the early 60s (the general preference for late Beatles over early Beatles, for example, reflects a general perception that the music of the late 60s is just cooler). When people do hear J&D, they often don't get it (i.e. they mistake the humour and subtlety for a lack of quality).
Finally, a more depressing point is the state of Jan after the accident. I have sometimes wondered what would have happened, in terms of the J&D image, had Jan died in '66. There are plenty of examples of distinctly average acts who secured immortality by dying young. There just is something irresistable (in a marketting sense) in the "live fast die young" image. But battling disability, while moving and admirable, just isn't "cool", it doesn't fit the Rock n Roll stereotype - which is I suspect one of the reasons why J&D so quickly disappeared from the musical consciousness. The halfwits in the RRHoF can't see past that - although I hope the release of Carnival might help to change that.
There is a very touching scene in Bob Greene's "When we get to Surf City", when Dean asks Bob about the RRHoF, saying that it would be good for Jan. Too late, in that sense. And to be honest, when you see the trite that gets in, I wonder if J&D carry greater credibility by not being part of it. As jdman says, we have the music!
