I think they're distinct enough tags not to require a merging / synonyming (if that's a word)
For example, some questions tagged color that wouldn't make sense to be color-scheme are:
How to interpret wcag2.0 guidelines on contrast for buttons and icons
Correction in color model
Intuitive colour pickers for non-expert users?
Really, I think color-scheme is used more for aesthetic purposes, but color is for the meaning of certain individual colours and their specific impact on users.
The real problem though is with everyone spelling Colour wrong!