There's nothing wrong with liking a villainous character and there's also nothing wrong with relating to a character on an emotional level, despite/and acknolowging all the evil things they have done. However, when fans start denying evil deeds with 'but they were just misunderstood' 'if only they understood' type speeches, that's when my gears grind.
I agree fully with that. Though there are villains that actually aren't completely terrible that you can feel sorry for. I mean, look at Heinz Doofenshmirtz. Sure, the loss of a toy train would have sent him over the edge and actually make him full blown dictator evil. But for the most part, his "villainous" activities are mostly either brought on by his family treating him worse than crap when he was a kid or some other odd petty annoyance. All psychological things. In later issues, it's clear that the "good guy", Major Monogram is just trolling him to the point where he sends in Agent P to harass Doof for going about his daily routine. On the other hand, Doof
loves his daughter and is fiercely protective of her (once shouting at a guy checking her out that She's 16!"). He also has a complicated relationship with Perry that suggests that he's his best friend.
Now, that's a clear parody/deconstruction cartoon villain, he can be a jerk, but he's such a sad little pathetic guy that you can't help feel sorry for. And he
is much more layered than most villains.