Here is a really good site on the rainbow phenomena ...
http://my.unidata.ucar.edu/content/staff/blynds/rnbw.html Red's at the top of the rainbow because of its wavelength and bend it goes through at the back of the drop of water.
As for chakras and colors that's got to be "higher" chakras equal higher vibrations equal higher (frequency) color stuff. The older literature does not give the colors so simplistically, but rather mentions things like silver and red together for a particular chakra.
Some people try and make a correspondance between the chakras and the notes of the western musical scale, which is another arbitrary association.
It would be interesting for anyone out there with "second sight" who can actually see auras and chakras to describe what they experience. I have no direct knowledge.
