There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy.
There can be different paradigms of how these things work, and I'm not saying it has to be in certain way. I generally prefer highly magical settings to also be fundamentally magical though, instead of merely being normal world + magic. This means that there are not modern physics to be discovered, not necessarily even chemistry. On fundamental level mystical principles govern the universe. The world is made out of four classical elements or is the dreams of primordial First Gods or something like that. Perhaps the flint makes fire because they're are shards of Volcano God's heart, or perhaps because an ancient pact made by the first men and the fire elementals. Just think how ancient people believed the world to work; well in fantasy those beliefs can be true instead of our modern science.
This BTW is not how my brain works naturally, I'm pretty science-minded person, but perhaps exactly for that reason I find such esoteric metaphysics appealing.