It's used for things (like hydrophobic molecules) that avoid other things (in this case water) as if they fear them.
Unless we're doing one of those "literally literally means figuratively" things here in which case... meh?
Just to be crystal clear here, I'm not saying we don't have groups who are anti-X for whatever value of X. I'm saying that recasting (and often miscasting) that antipathy as (maybe masked) fear is counterproductive.
> Specific phobia is an anxiety disorder, characterized by an extreme, unreasonable, and irrational fear associated with a specific object or situation.[1][2] Specific phobia can lead to avoidance of the object or situation, persistence of the fear, and significant distress or problems functioning associated with the fear. A phobia can be the fear of anything.
Whatever the term originally meant to the greeks, it does seem to be knit with the concept of fear today.