A scale (major, minor, etc...) is nothing more than a pattern of notes. The pattern states the distance between them - usually half-steps or whole-steps, but not always.
The root of a scale is essentially the "focus" of that scale, or (as slim said), the "home" for the scale. This can also give you an indication of which scale tones should have more focus than others.
A C-Major scale has exactly the same notes as a D-Dorian scale, or an A-Minor scale, or a B-Phrygian scale, etc...
However, if you are playing a C-Major scale over a C-Major chord, you are most likely going to focus on the 1st, 3rd, and 5th scale tones, as these make up the C-Major triad.