some problems are complex and comments and class hierarchy on a text file might not be enough to understand the problem. a text file allows you to write only in two directions, up or down.
paper on the other hand provides you four dimentions and more expressibility. you can draw boxes, arrows from one thing to the other and illustrations. some problems require a more expressive medium than just thought and a text file, and nothing beats the good old paper-pencil combo at that.