In the days of the internet and fandom culture being online, most people have a good idea of what "shipping is" (or they're at least familiar with the concept, but they just don't know what the term is).
For those who don't know, shipping is when someone wants two people to be in a relationship, or they just like the idea of them together. Typically this term is applied to fictional characters in a book or TV show, but some people will apply it to real life people like celebrities or teachers in their school. For now, I'm gonna just talk about shipping in terms of fictional characters.
When you ship two characters, they don't necessarily have to be characters that get together in the story. For example, in "Avatar the Last Air-bender," there were plenty of people who shipped Aang and Katara, who did get together by the end of the series. But there were also a massive amount of people who wanted Katara to end up with fan favorite Zuko instead. Back when the show was still on the air, there were massive debates online that apparently did get ugly. I was only seven-years-old at the time and didn't have free reign of the internet so I had no idea that was even happening. The writers didn't even intend for there to be any kind of debate on who Katara should end up with, to them it was always going to be Aang from day one.
The easiest way to start a shipping war is to have a love triangle in the story. We all remember the Team Edward and Team Jacob debate right? In every shipping war, whether it was intentional or not, there's always gonna be a more popular ship. More often times than not the more popular one will win (maybe so the author doesn't have to deal with too many angry fans). But it can stink to be supporting the much less popular ship, especially when it doesn't come to pass.
(Warning, spoilers for "Once Upon a Time" and "the Mortal Instruments" below)
When I first read "the Mortal Instruments" series I was really rooting for Simon and Clary to end up together. One because Simon is my favorite character in that series and I'm a sucker for the childhood friends become lovers trope. Needless to say, that did not happen. And while I had been disappointed, Simon eventually found happiness with Isabelle and Clary and Jace do make a good couple, especially since now we know they're not actually related and Jace is over his teen angst.
Though the ship that never got together, that I'm still bitter about to this day, is Emma and Neal on "Once Upon a Time." Only recently have I been able to watch Neal's death scene without sobbing like a baby. When I first watched the show I had a feeling they wouldn't be endgame because Emma and Hook are a very popular ship and I was really annoyed the writers just went with the ship that was more popular, probably because they didn't want to loose ratings.
Just to be clear, I'm not hating on anyone who ships Emma and Hook, they are a solid couple on the show and I can see why so many people like them. I just personally think she and Neal were a stronger couple. It just kind of stinks being in the minority of this love triangle because so many people are quick to point out Neal's flaws, using them to claim why he'd be a terrible boyfriend for Emma, while completely glossing over Hook's. For example, most people are quick to point out Neal was a thief when he met Emma and was a "bad guy," but stealing is really the worst thing he's ever done. Hook on the other hand had murdered people, including his own father. But it's okay because he's "hot."
Having different opinions about ships is great, it can spark interesting debates and I love hearing other people's reasons for loving or hating a certain ship. It just can be a bit frustrating to be in the minority. It makes it really difficult to find good fan fiction about by favorite couples.