I am a little fuzzy on the whole "good/bad" thing. I admit this freely, and I'm not being sarcastic. I have personal standards of "good" and "bad", but they're quirky and not always consistent.
One of my biggest problems with genre fiction is a tendency to excuse horrible things that a hero does because they are wearing a T-shirt that says "hero"- or, as I believe they'd put it over at TVTropes, holding the hero ball. It's not the excusing as such that bothers me- I am certainly capable of special pleading on behalf of characters I like. The thing that bugs me is some variation on. "it's okay to treat character X that way because character X is just an orc/a vampire/a Dalek/whatever." Deception, abuse both physical and mental, petty cruelty- all excused because the target is "bad." It absolutely drives me up a wall. Almost inevitably, we are later asked to hate the villain characters even more because they have the gall to treat the hero characters exactly as the heroes have treated them.
I prefer to read about, sympathize more with, and even admire more, characters who don't try to excuse their assholery with this kind of rationalization. I would much rather hear "yeah, I lied to him, and I'd do it again" than "I lied to him, but it's okay because he's bad."
A related complaint is this: I don't like it when heroes spit in the soup. If someone invites you over to dinner, you don't go into their home and then spit in the soup. You just don't. It doesn't matter if someone is a complete monster, in personal action as well as species. By accepting their hospitality, you've agreed to put that aside. (The same goes for offering them hospitality.) In particular, there is one scenario guaranteed to get me rooting against a hero faster than any other.
As happens, a hero and a villain are teaming up, to fight against a greater threat or just because the author thinks that would be cool or whatever. There's some downtime, while the truce is still in effect. The villain makes some idle, polite chitchat- the key here being that it's not a veiled threat or a deliberate attempt to needle the hero. It is, honestly, just making conversation. "I hear the Mets are gonna suck this year." And the hero gets all snippy and starts going "we're not friends, you suck, I am super super better than you."
That's when the little voice in my head starts rooting for someone to fuck the hero up, really really badly.
(And then there's the one where the hero gets all mad at some character who gives him a boner, just because she [heteronormative bias!] disturbed his equilibrium. But at this point, I should just do a post on how much I want to see Harry Dresden get the full Prometheus.)