I recently had some people plaguing my Crystal Guidance Facebook fan page. One lady was puzzled how I would suggest a blue or purple crystals (generally Third Eye) with the red Root chakra. While it was an excellent question, I choose not to answer it since she was just attempting to cause problems. (In another location she proceeded to call me a stupid bitch that I didn't know what I was talking about. But that's a whole other story.) Yes, the chakras have a primary color and a great general suggestion is to balance that chakra you can use a coordinating color. However, that is not a strict rule. You can use any color you want on any chakra. In fact, if a chakra is over-active (too much energy) then you want to use a complimentary color. In this case, too much Root energy you would use blue.
An example for this is anger. Anger is related to the Root chakra (red). When you think of anger you even think of the color red. However, red is a very active color. More red energy will not help you to calm anger. In fact, it can have the opposite effect. In this case you would want to go for a calming color. Blue Lace Agate, a light blue color, is an excellent one for calming anger. (See more crystal suggestions for calming anger.)
The most important thing is for you to follow your intuition on what works for you. You do not have to match the chakra color with the crystal color. It's not necessary. However, it is a great place to start if you are trying to get an idea of the basics. Follow what works best for you.
I have created a chakra information page on Crystal Guidance. It has a photo of crystals that are related to each of the specific chakras plus a little info on each of the 7 main chakras plus 3 of the transpersonal chakras.