I'm pretty sure it's meaningless. I bet for most of the people when they received their headbands they just accepted it the way it was and didn't care about the color.
The only possible thing I can think of would be it shows what you're best capable at (Taijutsu, Genjutsu or Ninjutsu) but after thinking it over, why would you want your enemies to know what you're good at?
I would love it if someone had a Tye-dye headband. ^_^