When I learn new theories in class, often the first thing I think about is how they can be applied to fiction and fandom. "So when Anakin did this, this is what was happening in his head... If Padmé were to do that, this is how she might justify it to herself; these are the defense mechanisms she might use..." Occasionally, there's also "So this is how the jury will feel about my client, and this is why, and this is how I might be able to change their minds...". It's how I avoid getting bored, but it doesn't help me remember the details I need to know to do as well as I'd like on exams, details like the name of the theory's author. In fact, it's really distracting. But I'm not a Ravenclaw; I don't enjoy knowledge for its own sake. I estimate the value of knowledge by its usefulness.
Sometimes I find myself going beyond applying psychological theory to fiction and fandom. Sometimes I come up with whole new theories in attempts to understand phenomena like shipping. Today I'm going to talk about two such theories. They are based, we could say, on a case study of the case I know best: my own. (The caveat is that this case is rarely representative, as I realize the more I learn about what is considered normal.)
Learning psychology has helped me be able to empathize with, i.e. understand and see from the points of view of, people real and fictional who are different from me.
For example, I used to ship Harry/Bellatrix. I didn't grasp the reasons it wouldn't work and what kind of relationship it would be if it ever did. I failed to relate to Harry, to understand the depth of the hurt Bellatrix caused him when she killed his godfather, and how this hurt would realistically prevent him from being able to feel anything positive towards her. I didn't empathize with Harry except at certain moments in the book; fundamentally, I didn't understand his personality or see from his point of view, which is what's meant by empathy (not to be confused with sympathy, a.k.a. compassion).
I also failed to empathize with Bellatrix, to understand why her having any positive feelings about Harry doesn't make sense, given that he is the mortal enemy of Voldemort, who is the center of Bellatrix's life. She fanatically loves Voldemort and his cause (which in her mind are one, anyway), and this would automatically make her fiercely hate the enemy of what she loves. For Bellatrix to feel attracted to Harry, and worse, act on that attraction would be out of character. No, that's not right. We don't control who we are attracted to. But when the attraction we feel is so unacceptable, we tend to repress it and keep it outside of our consciousness, so we either don't feel it, or don't realize we feel it. (The latter possibility contains some intriguing shipping potential, doesn't it?)
Once I'd learned to empathize with both characters, I realized that Harry/Bellatrix can only happen, arguably, if one or both of them are out of character, and that it can't be anything but angst. I mostly lost interest in the pairing at that point. If I had continued to ship it, then I would be demonstrating a failure to sympathize with one or both of the characters. I could ship it while fully understanding how awful it would be to love or desire someone who has hurt you so much, and/or someone who is the enemy of everything you stand for. I could understand all this and not care, or even like it precisely because I understand how awful it would be for the character(s). I ship a lot of pairings like that: for example, my Star Wars OTP. The intensity of the angst is what makes me enjoy such pairings.
Failure to empathize with a character results in that character being OOC in your fic. Failure to sympathize has no effect on their characterization in your fic.
Now let's look at the flip side of shipping: the anti-ship. The pairing(s) you can't stand, the ones that make you gnash your teeth, the ones you hate with the intensity of a thousand suns. Maybe there are no pairings you hate that much. I have an idea why, too. It's, again, about empathizing with characters.
Has it ever happened to you to relate to a fictional character so completely that when you write from their point of view, the lines blur? The lines between them and you. You are that much alike. They think exactly like you do. You don't need to think hard to understand them; you don't need a lot of info or dialogue or scenes in the book that show you what's going on in their head, because you had already guessed, and guessed right, every time, from minimal clues that no one you know even noticed. You don't need to learn to understand them - you have always understood them. It's more than empathy. You know that in the exact same circumstances, you would have done exactly what they did, and made the same mistakes they made. You know how they would act, think and feel in any situation - it's the same way you would. The only differences between you and this character are differences of opportunity.
Maybe there is no fictional character who is that much like you in personality and way of thinking. It's rare and amazing when it happens. I would be surprised if anyone found more than one fictional character they saw themselves in to this extent. It's disconcerting when the creator of a fictional work gets you so deeply.
More often, an illusion of this happens where you think a character is just like you, but in truth, while you share several personality traits, there are important differences between you and them. You may think, for example, that you are just like Harry Potter; you identify with him throughout all the books, but you can't see why he would fall in love with Ginny, and you think it was OOC. It wasn't. It's that you are less like Harry than you think, and if you are writing fanfic about him, you have to be extra careful to stay aware of the differences between you and him. It's hard not to let the similarities make you lose sight of the differences.
But what about when there isn't anything a character does or thinks or feels that you can't automatically, immediately understand, anything that you wouldn't do or think or feel if you were in their situation? When the identification happens instantly and is total. When writing them isn't like mentally putting on a mask - it's like taking off all masks. Can you imagine that? (Scary at first? You bet.)
Now imagine reading a fanfic in which the character you automatically and completely relate to falls in love with someone who, canonically, did something terrible to them, something terrible that you feel as if it was done to you, because while reading about them or seeing them on the screen, you virtually are them - their emotions are your emotions. That's out of character! you might think about the fic. He/she would never love X. But it's deeper than that. Your reaction to the ship in question is visceral, emotional, physical. It's irrational and outside your control. It can be rage, horror, disgust. It's a NO from the depths of your soul. It's a white-hot hatred of the ship in question. A hatred so strong that you find it hard not to hate everyone who ships the pairing. Is this what makes people (people more expressive and impulsive than me) participate in ship wars?
Mystery solved.
If you've never felt that kind of hate for a pairing, I hypothesize you've never experienced that extent of fusion with a character.
The theories above are entirely untested. I have no idea if they accurately explain these things for anyone other than me. I'm curious to know if they do.