I think the main reason people don't like Eldar are that they were OP on the tabletop, they're extremely smug pricks despite never really getting any major wins to back it up, and they make the Imperium look bad morally (same reason Tau are hated). Sure, an Eldar will kill billions to save a handful of their own, but that's still better than the Imperium, who will kill a billion of their own to kill a handful of xenos, even if said xenos don't pose any actual threat. Many Eldar will show some remorse for it too. Finally, I think a lot of fans just don't like the aesthetic. They don't like a bunch of pretty space elves in power rangers gear in their grim and dark space gothic future.