Authors of content and programs with ligatures-by-default subject their readers and users to the penalty of ligatures.
Some people like pain, but that doesn't mean we need pain switches on everything with pain set to on by default.
That's you, and not very generalizable. Many people edit on sites with ligatures and many people edit non-Latin text where isolated, non-ligatured text is wrong (Arabic, some Indic scripts, Han characters, Japanese katakana).
Me personally, with respect to code, I pretty much think in terms of tokens: to remove the `==`, I backspace twice, rather than that to remove the `==`, I remove `=` and then the other `=`, and each requires one backspace.
It's obviously personal preference, because many people prefer it. If I found ligatures harder to read or edit then I wouldn't use them, but I don't, so I do.
> programs with ligatures-by-default
Such as?
To be honest though I think I like those big fat commas the best. As someone pointed out, using dot and comma as semantically important in software is a mistake because they only differ by one pixel.
> It being good or better is science
Citation needed.
people likely prefer them for aesthetic reasons, just like they do certain color schemes, but there are objective answers in regards to legibility, and many people certainly use suboptimal setups. Lots of people code sitting hunched in front of their computer too, which is their personal preference, but also objectively bad for your neck.
Ligatures suffer from some straightforward objective issues, like being semantically wrong in certain cases. An inequality check should be a ligature, but in a literal string the character sequence is likely not intended to be subsituted. As such they create unecessary ambiguity, which is just bad.
Also they functionally don't have a reason to exist in monospaced fonts which are the norm in coding. given that The issue they're intended to address is overlapping characters.