If the bare roots are down along the sides of the tree's original root ball from planting, by all means cover them. However, if the roots are running along the surface of the ground, it's probable that the tree did that itself. Some trees are naturally very shallow rooted and others tend toward shallow surface roots when growing in heavy, compacted, or wet soils. For aesthetic reasons, you can add 1-2 inches of soil on the surface and another 2 inches of mulch OR 3-4 inches of mulch. Trees can suffer (imagine their roots smothering) if their surface roots are suddenly buried several inches in soil. That's why I'm recommending you keep the soil/mulch (1-2 inches plus 2 inches) or mulch only (3-4 inches) layer no deeper than 3-4 inches total.