Sure. Go to your common/landed_titles.txt and search out the title's color you want to change. You'll see two entries labeled 'color' for each title, color1 and color2. You'll want to change color1 as it is the main factor in determining what color represents your faction on the map. It goes on a RGB scale of 0-255 for each of the three value. If you want, you can copy colors from other factions or just experiment to find the mix you desire.
color2 is almost useless, so much so that some factions do not have an entry and those that do are all 255 255 255. I'm not entirely sure what it does to be honest with you.
edit: Here's an example -
I changed the color entry for the Kingdom of England to this:
k_england = {
color={ 0 26 26 }
color2={ 255 255 255 }
Which on a RGB scale would be near black, and sure enough:
Happy modding!