I think you've got it backwards. Incest and loli and shota aren't popular despite the controversy. They're controversial in part because they're popular. If they were unpopular, not much of it would be made, and there would be a lot less of it for people to get upset over.
Controversy aside, why is this stuff popular then? I think it's the element of the taboo. The forbidden fruit. Incest and underage sex is immoral, so people indulge their fantasies by way of fiction instead which is a far, far healthier and saner outlet than doing so in reality.
Not that people would start molesting their little sisters if they didn't have this outlet, though a few might. Just like not everyone who plays violent video games is a latent serial killer, and not every lonely housewife who reads rape-fantasy smut novels hopes they're sexually assaulted by a stranger in a dark alley. Fantasy is fantasy. Just about every mentally sound individual understands there's a distiction between fantasy and reality.