When writing programming code, markup, or any other structured text of that sort, it is easier on the eyes and to parse mentally when vertically aligned. At least when reading English characters left to right, top to bottom. (I don’t read much else in that capacity).

Whereas with the written word, letters flow into each other, to give a better reading experience.

As for ligatures, having != (not equal), <= (smaller or equal to), == (equal), === (extra certain we’re equal as we messed up the implementation of ==, but need backwards compatibility) or similar operators show as the symbols they represent (while still maintaining the correct spacing), is more comfortable when ingesting large amounts of code, to me at least.