RWF has always been a hard sell. Sarris in the Voice and Canby in the NY Times were early and constant champions as well as Manny Farber. Kael ignored him, and her acolytes have not done much better.
Even many good critics seem to get hung up on what is percevied as Fassbinder's "love of cruelty." While I will admit his films are often steeped in cruel behavior, I don't think he particularly loved or savored it. He just knew that it was one of the major fuels of human existence and was determined to bear witness to this fact. There are also distinct (if sometimes faint) traces of hope in his work. RWF may not traffic in transcendental joy, but it is not all gloom and doom.
Fassbinder also came on the scene at the tail end of the French New Wave which had offered up a very different view of humanity. For many critics and film goers alike, the French New Wave was their first love in film and had opened their eyes to the possibilities of cinema. Farber perceptively realized that one of Fassbinder's merits was that he was a filmmaker in a new key, especially in moving away from Godardian cinema. With Fassbinder, we move from magical Paris to grubby Munich and not everyone was happy about the switch.
Even gay critics had problems. Here is a link to an exchange about FOX AND HIS FRIENDS:
http://www.ejumpcut.org/archive/onlinessays/JC16folder/foxandFriends.html
Andrew Britton was in general a perceptive critic, but he had a blind spot when it came to Fassbinder (as did Richard Dyer). Fassbinder was not the right kind of queer for them: he kept committing sins of cinematic bad manners by showing that queers can be as nasty as non-queers. Lions and tigers and bears! Oh my!
The pendulum has begun to swing back in the other direction, but Asian cinema has been the focus of critical gazes lately, so RWF gets lost in the shuffle: he does not have the nostalgic appeal of the French New Wave nor the Tarantino cool quotient of Asian cinema. He also specialized in that most despised genre -- the melodrama.
But he is acknowledged enough that he cannot be just dismissed out of hand (Atkinson is careful to posit that the problem is in him and not RWF, though he is trying to give his readers a way out of grappling with RWF without feeling bad about themselves).
One other thing to add is that the fairly regular revivals of Fassbinder's films that play in NYC are usually packed so the problem may be that critics have to catch up with audiences. Heck, BERLIN ALEXANDERPLATZ is #156 on amazon in sales (though well behind the second season of Perry Mason).
Brian