During the 2000 election debacle, my recollection jibed with yours so I looked at some materials from earlier elections. Color assignments in earlier elections were not consistent; while I agree that blue for Republicans and red for Democrats might be ideologically appropriate, this is not the first election where Republicans have been red and Democrats blue. BTW, I found it interesting that in the 1996 race the networks used shades of red and blue which were indistinguishable on a black and white television set.
I never could quite figure out why people were getting so exercised about the color choices after the 2000 election. I recall that different networks had differing colors for the (R)s and the (D)s in the same election.