It's because of two reasons in my experience and my observation;
The fanservice factor in which the two characters could be completely mismatched to the point of being toxic for each other and not even have the orientation necessary to be romantically involved yet fans pair them together because they look hot in which case the pairing works more like a Playboy video than a deep meaningful romance. The couples in this scenario are usually only physically attractive or cool, and have many other fetish factors behind them being together. I've even seen fans go down roads I dare not speak of here.
The wish fulfilment factor (I'm guilty of this one). Sometimes, we see two characters who have such great chemistry or a character who we know will make someone happy, we just want it to happen because we love these characters so much, we want to see them be happy. These couples usually have better chemistry and are a lot healthier. Plus they tend to feel more natural. Yes, sometimes, you'll get some that just don't work or are debatable, but the basis of these couples is usually either the fan is a romantic (like me) or we love our characters and want them to be happy.
Usually, shipping is harmless though some fans can get a little aggressive about what they believe should happen. My advice is to just leave it alone, ignore the people who bother you or make problem content, and just do your thing while being kind yourself.