Literary and historical references to reds has always meant communists. Young people will read these pre 2000 references and think that they refer to Republicans. The propaganda press flipped the colors for the two parties in 2000 knowing exactly what they were doing.
I disagree. I think they flipped the colors to be more aligned with military terminology. Blues are friendly, reds are hostiles/the enemy.
Look at it that way, look at the media and suddenly it makes a lot more sense.