Supernatural, like most dark fantasy/horror media, inhabits a basically Christian universe - very Catholic, from what I can see. I don't think other types of Christianity use holy water. That's why crosses and holy water and Christian exorcism words work on the demons.
Dean uses these things all the time. Dean knew that the water Bobby threw on him was holy water. He *knows* holy water is effective on demons. He knows this empirically.
How can he know that holy water exists and not believe in holiness itself? How can he know that there is darkness and not believe there is light - where does he think the tools to fight it come from? How does he think holy water happens? (How DOES holy water happen, btw? Is it just tap water blessed by a priest or are there rules about it?)
If there are demons, there must be angels - especially since Christian mythos has it that demons *were* angels who rebelled. Okay, Dean isn't a supergenius, but he's not stupid and he does employ logic on occasion. If there wasn't a heaven, his arsenal wouldn't work.