I don't think it will hurt the tree to cover up the roots. Two of my oaks are in a low spot, and over the years the topsoil has washed away and left roots exposed and hardpan ground that doesn't want to support grass. Putting those beds in has helped solve a couple of problems.
Where you run into trouble with trees is banking soil up against the trunk. The problem with that is you provide soil dwelling insects a new avenue to attack the tree. Additional moisture on the bark may also be a problem.
It has been mentioned downthread that the size of my trees is going to allow me to put some soil around the base without causing many problems. As the beds have settled in all of the rain, we've pulled a little away from directly touching the trunk, and there is only a couple of inches left. I have placed some insecticidal pellets in the soil around the trunk and hope that it will help, but I will keep an eye on all of the trees to make sure that no problems crop up.
Thank you. Could not remember what I needed to worry about with filling around a tree and it was, as you said the soil on the trunk.