We've heard the phrase "Baptized in blood", but it's highly doubtful that the term was meant literally. Dexter Morgan was a baby when his mother was killed. Dexter was left to watch the murder and was found covered in blood in a storage container. Thankfully he had someone smart enough to know that a traumatic moment like that would have some kind of long term affect and took him. Well, that and because Dexter was his illegitimate child. Either way, Dexter grew up learning the right and wrong people to kill. But any which way you slice it (Pun intended), Dexter is not a good person. But can you really judge what he does? Yes and no.
Here is the funny thing about Dexter, he is one of the few people who straddles the line of hero and villain almost perfectly. Yes, he only kills killers, but he is still a killers. So does that make him bad? Everyone reading would more than likely be ok with someone going after the person who killed their loved one(s) if the law system didn't work. It's not like Dexter is going around killing jay-walkers or teenagers walking through a gated community with skittles. Dexter kills the worst of the worst and he does so much prep work that there it's rare that he gets a kill wrong. Rarely being the key word.
Here is the problem with Dexter, he has killed or has been directly the reason why innocent people have been killed. Sgt. Doakes (SURPRISE, MUTHA ****AH!!!) and Lt. Laguerta are perfect examples of people who have got caught in his whirlwind of lies and shenanigans. Now you're probably thinking that it isn't his fault that people die in his search for justice and need to silence the monster inside of him, but it actually is. The most important thing about Harry's Code is planning. This planning is supposed to keep innocent people out of harms way and keep the wrong people from dying. Over and over Dexter's emotions have gotten the best of him and caused the people around him pain and death. Which is funny because he is supposed to lack emotions. Eventually Dexter realized he was the problem and took care of it (in the worst series finale of all time), but not before the death of his sister and his wife.
As much as we all want to love Dexter Morgan for taking out the scum of the world, he's selfish. There have been multiple times when the options have been turn yourself in or someone innocent will die and he has chosen himself over the innocent person. There is always an exception to Harry's Code or he tries to justify what he's doing because he wants to understand something further. The Trinity Killer was a perfect example of someone that should have died way before he got the chance to kill Dexter's wife Rita. Granted, she was very annoying and no one missed her, but that is far from the point. Dexter should've killed him. But instead, he let his curiosity get the best of him and Trinity went on to kill more people and that included his wife.
At the end of the day, Dexter may have killed a ton of people that were absolutely better off dead, but in exchange there have been innocent lives that have been lost in the process.