Layers allow for a much more versatile, non destructive workflow. It's a lot easier to achieve complex, layered effects and lighting using multiple layers rather than a single one. I don't use as many layers as other artists I've seen, but a specific set of layers are essential to my pipeline. For instance, I'll have flats on one layer, then each light on a separate layer utilizing various blending modes, then shadow grading, scene light grading, then total scene tint to pull my palette into line. Inks go on top, then a folder of post effects like sparks, glow, fog, bloom, etc. above that, and final levels.
Layers are also just useful for splitting certain things out as I draw them. For instance, if I know certain inks are going to be color hold, like glass for instance, I'll split them out into a different layer as I'm drawing them. Then I can move that element around in my layer stack and recolor it as I see fit. Sometimes I'll lay down flats for various scene elements in different layers if I know I'll need to select an element later. For instance if I have a scene where there's a woman in the foreground against a foggy background, I'll put the woman in a different flats layer than the background flats so that I can just select the woman with a single click to mask out the fog in the post layers. Huge time saver if you're doing complicated stuff!