You can safely cover emerging tree roots with soil or gravel. Just don't pile earth or gravel up against the trunk of the tree. The roots are rising to the surface because that is where they find water. Try watering deeply after you aerate so the water does down deep and the roots will follow. Frequent shallow water sessions bring up the roots. Crushed rock might work great - you can add container gardens or maybe a groundcover. Keep growing, Marianne Binetti