For me it depends on what’s being written. For the stuff I work with day to day (all very “boring”/mainstream languages) there’s no possibility of ligatures causing confusion, and I find them to be an enhancement in both aesthetics and readability.

I also think it would be interesting if a programming language used the Unicode characters that ligatures simulate rather than combinations of general purpose characters, but that seems unlikely given that it’d require a new programmer-oriented keyboard layout.