Hating the Heroes
(If you haven't already, you should read the "Loving the Villains" post before this one.)
Two other iconic characters of the same franchise: Luke Skywalker and Han Solo. Their names, really, say it all.
Luke Skywalker. His first name was popularised in the first few centuries CE by one of the Gospels. Even among the Gospels, the Book of Luke boasts the best Greek grammar, is reputedly written by a doctor, and is obviously a work by a writer of high religious ideals and literary skill; a rules-follower, who wants to get every detail correct. His last name evokes powerful images as well: walking across the sky, from cloud to cloud, like an angel. If this seems a stretch, consider his looks: blonde, clean-shaven, dressed in white and wielding a saber of blue light. He's an innocent boy. An orphan, or so we think, and his ideals remain unshaken.
Then there's Han. "Han Solo" means, literally, "man alone" (Korean and Latin). He's a loner, a rebel ("You don't want to know him!"). In literary terms, he's a Byronic hero. A rogue. And yet... in the rivalry for the love of the princess, Han wins out (let's just say that this is best in the end), and we're happy about it. Luke runs toward doing what is good. Han needs to be dragged there, only reluctantly turning from his own problems and goals to fight for the greater good, and the woman he's come to love.
Of the two characters, Han Solo has by far gained the most popularity. Luke, by contrast, has even attracted a substantial anti-following. I think it's because Luke is too good. Who can relate to that? He's okay. We might not hate him for it - but we still perk up when Han steps into the room. There is no controversy in Luke, whereas the phrase "Who shot first?" evokes in fans a lively debate (for the record: totally Han; and I would have too). Han is gone (sorry for the spoiler there), but there is hope for a darker Luke in the movies to come. The cloak (maybe a hint of the emperor?), the hand (definitely a hint of Vader). They're darkening the golden boy, and I, for one, am excited to see it happening. In the same movie, the up-and-coming villain is tortured, torn between a will to gain power in the Dark Side and the pull of the Light Side. He is definitely a baddie, but like his father was a good guy with an uncomfortable tendency to criminality, Kylo Ren is a bad guy with an uncomfortable pull toward the good.
In my own writing, Danny Wolfe is obvious. The guy's in a dark place, and there isn't much in the way of light ahead of him. Marina Saalik is a tortured soul, burnt by life and afraid to love. Her dark side is something she'll need to hide or tame, but I wouldn't hold out a lot of hope for that. I've been in a room in which readers were arguing over Eric Dirridain (Crogmoor), defending or condemning him as if he were a personal acquaintance who'd done an exceptionally stupid thing. And in the end of that book? Let's just say those who cried out in disbelief will be even more engaged when the third one comes out.
If you can tap into your own faults - not the easy stuff, but the deep crack in your character that makes you understand both grace and condemnation - and if you can put something similar into your protagonist, then your character will come alive, will engage... will become a real person in the experience of your readers. That's what we're looking for.