I believe that media tradition was broken when USA Today published its map that way for 2000 and started referring to red state people as Republican and blue state people as Democrat. The political punditry quickly followed suit. We haven't had any elections since that would show if Republicans have been perpetually designated as red or if red still symbolizes the incumbent party. In '04, it could have been either.
Actually, on election night of 2000, a lot of people on FR kept decrying the fact that the MSM displayed maps that used the red designation for Republicans.