Oh not at all, in fact I think the most of the hate comes from 'hardcore' comic fans. They know all the villains in the show and probably don't think any of them are that obscure at all. I have to say it's probably not the best written show at all, but that might just be me...
I think it might be a case of "That's not how it is in the comics!" syndrome.
I talk about the show with quite a few comics people. Several find Young Justice formulaic (You thought you beat the bad guys... but it was really all as planned ! Ha! Ha! ha!) and a lot of the characters poorly characterized (M'gann and Superboy in particular get flack), not because they aren't like the comics, but because they're just really not well done (in their opinion). They appreciate the villain choice and are actually big fans of their use of The Sportsmaster, the Reach, and many others. All that said, they don't hate it.
A lot of them enjoyed the last work of Greg Weisman (which also got cut after two seasons), the Spectacular Spider-Man, quite a bit more. That diverged fairly greatly from comics as well, but they found themselves just really invested in the characters and the story arcs.
