Agreeing with Vladimir here, I would cover them up to the point that they meet the main stem, but do not cover the main trunk.

I would not cover, I prefer aesthetics before before anything else :D

In fact, I would do the opposite: cut those smaller roots emerging from the thicker ones. It would not kill nor harm the tree, but it would probably slow down the growth a bit. It depends how big the rootsystem is.

That's my opinion, and remember, I live in northern country and my 'trees' are still small. It wont hurt the tree to be barerooted, but covering them up should encourage more root growth from those thicker roots.

I would not cover them. It is believed by many commercial citrus growers that a small portion of the root structure should be slightly above the soil line.

OJ: Why?

I think to prevent root rot they should be exposed slightly. Although chances are small that root rot will occur just from covering all those roots, some people might not want to risk it