i'm not so sure that's true... eraserhead as definitely a surrealist nightmare (though i guess it could be dismissed as an arty college film). but blue velvet had its fair share of detractors at the time...not so much for it's complex plot, but lynch definitely had the reputation of being a bit out there/pretentious/surrealist/etc. mixed reviews for velvet, if i recall, and definitely a lot of people who hated dune.
if anything, i think lynch has proven himself these days, or perhaps seeing his influence and direction come to fruition has helped his films age gracefully and be viewed as classics. either way, fire walk with me is a must to watch upon completion of the show!