From everything that I've heard, the roots filter out 99% of the food colouring, and you'd have to use a lot of it anyway. Kind of a waste.
What you CAN do, however, is colour them after harvest. Take buds with long branches. Make a clean cut on the stem, and then put them into a container mixed with water and a LOT of food colouring. Just as you would put a flower into a vase. Without the roots, the plant still functions for a while as it normally does, and should drink up the water, dye included. This will turn everything on your bud your desired colour.
Props to fdd on this. He's the one who enlightened me to the fact that it couldn't be done through the roots. I think he has a few posts regarding this; you might want to look them up.
::EDIT:: His thread is linked in the post above mine.
~Ethno