Shipping has been a part of fandom since pretty much the beginning, when fans would mainly communicate through fanzines and snail mail. Imagining characters as couples is fun, even if it wasn't the creator's intention and would never be canon.
However, the fun aspect of shipping seems to have eroded over the years. Shipping has become a life or death affair, with ship wars cropping up in every fandom. A ship war is when rival shippers resort to bullying and harassment against each other.
I can't say for sure when this started because I haven't been involved in fandom for very long, but I'm sure the Internet and online communities has something to do with it.
The Internet is a great thing. It allows people from different places and walks in life to come together and talk on equal footing. However, like anything else, it can be abused.
One notable example is when an Undertale fan artist accepted a cookie as a gift from a supposed fan, and when she ate it a needle pierced her tongue. The suspected motive is that the "fan" didn't like that she shipped Sans and Frisk.
There have also been numerous cases of fans sending death threats, doxing people (releasing their personal information like real names and addresses to the public), harassing fans and creators to the point where they're forced to delete their social media accounts, all because of shipping.
This is inexcusable. Fandom was created as a way for those that society normally rejects to find common ground with each other. Now it's become a minefield unless you stay in very small circles.
There is no excuse to attack people who have opinions that you don't like. You can mute certain filters on most social media sites, or find a plugin that will allow you to.
I understand feeling like you have to say something if a ship is morally questionable, such as in the cases of incest or pedophilia. I don't like those kinds of ships either and I do my best to avoid them.
However, giving your two cents and directly attacking someone else are two very different things. Lots of people use fiction to explore concepts that are taboo in reality, and that doesn't necessarily mean they support the real-life counterparts of those concepts.
That doesn't make these concepts right and it doesn't mean that there aren't real perverts in fandoms. There are creeps everywhere and if someone is acting like a creep you are well within your right to block them and, if they are breaking the rules of the platform, report or ban them.
There is another disturbing trend of fans demanding that their ships become canon. This is most often seen in "Voltron: Legendary Defender" today, but there are other fandoms that experience this problem.
Art is a conversation between creator and consumer, and alternate interpretations are what makes fandom so fun, but to demand that fan interpretation should be reflected in canon is unreasonable.
As a writer, if I took every piece of criticism to heart, I would lose my original style and intention. In trying to please everyone, I would end up with something that disappoints everyone instead.
Besides, fan works are what keep a fandom going. Seeing AUs and fix fics of my favorite stories is fascinating because it often reveals sides of the story I never even thought of, even if I don't agree with the changes wholeheartedly.
If canon were changed to match popular fan interpretation, there would be nothing to interpret, and the creative spark that fuels fandoms would be lost.