User blog comment:ImperiexSeed/Supernatural Mysteries/@comment-1509826-20120311211320/@comment-4920092-20120312180025

It's entirely possible he never thought about the how or why. To him, Holy Water may have just been a series of steps: 1. Say incantation 2. Drop Rosary 3. Hurt Demons

It's like driving....you can drive a car without knowing how it works. You can even fix a car without understanding the thermo-chemistry and the physics that correspond to WHY a car works.

That is, of course, speculation. Another piece of speculation is that Dean and his loved ones have always gotten the short end of the stick (the "family curse"), so he's incredibly skeptical about any benevolent power.