In the book Sir Percy drew a small red, star-shaped flower when he signed his messages; the flower was the pimpernel, the ink was scarlet (Chapter 7).
Pimpernel flowers can be many colors but perhaps the author chose the color scarlet to signify the red blood that flowed so freely through revolutionary Paris.
Wikipedia: "...mysterious Scarlet Pimpernel, takes his nickname from the drawing of a small red flower with which he signs his messages..."