I think people don't like it because it's not intuitive. When I hit backspace next to a character, I expect the character to be deleted, not for it to shapeshift into another character. I see how ligatures can be nice for some people, but it's definitely not as intuitive as showing the actual characters in place.
Also if I type two characters, I expect to see two characters - and not a single character that is somehow not aligned with every other character's columns. And because it is not aligned, the space left and right seems to be off. Everything about monospace ligatures feels unintuitive to me.
