The C major scale and A minor scale are completely different. Even though they have the same notes, they have a distinctively different quality to them. The difference is the root note. The root note functions as home base to what you write in that key.

Example: If you were to play an A minor arpeggiated lick over a C major chord, it's going to sound contrasting. A more consonant sound would be to use a C major arpeggiated lick instead.

Music is the art of sound, not what scales have the same notes in them. Each scale has it's own quality, and each mode is used to bring about a different quality to what the key might be.