I think this is born out of puritan ethics attached to counter-culture “pure” living. Essentially all desired outcomes must be earned through righteous, hard work. Anything short of this effort is cheating.
For me, it’s out of respect for the body’s natural methods of dealing with problems. Obviously there are some cases where it’s useful to interfere with the body’s processes.
But in general humans are extremely complex. We tend to think that we have a better understanding of things than we actually do. The human body does things that we still don’t understand fully, and unless there’s an incredibly clear understanding or benefit of some treatment, I’m hesitant to try to change it. Mostly because of how much I know that we don’t know yet.
If we don't know how the human body works, then surely we don't know that melatonin is better or worse for the body than not taking it. Perhaps it is worse, or perhaps it is better, but either way it has at least one positive effect.