Don, I think it's because the top three strings are tuned to facilitate a consonant harmony. The top three string constitute an E minor chord in third position. (Or a G6 chord). These are generally the chordal part of the guitar especially for beginners. The bottom three strings are in fourths which would constitute the movement of bass notes. The reason for this is that if you put an interval of thirds in the bass notes, you would have mud.

So it was arrived at to accomodate both the use of chordal and bass lines in combination. The lute, and it's antecedent the Vihuela have a slightly different tuning and does not accomodate the bass-chord approach as well.

Frank Hamilton