Negative Phototropism In Plants
The roots respond to gravity, not to light.  They display what is called a geotropism (aka gravitropism).  It has nothing to do with the light..  The roots grow TOWARD the force of gravity so the roots exhibit positive geotropism.   The stem grows AWAY from the force of gravity so it exhibits negative geotropism.   Think about a tree planted on a hill.

Phototropism is a plant's response to light.  It has nothing to do with the direction of room growth.  The stem may lean toward the sun (because of it's positive phototropism) but will still grow upward because of its negative geotropism.  

**If the light was below the plant, the roots would still grow downward.