To scramble is to move quickly in a disorganized fashion, like people running to get out of the rain. When you scramble a message, it can no longer be read.
Have you ever run somewhere, in a hurry, with no regard for how you looked? Then you scrambled. Quarterbacks scramble when they need to escape defenders trying to clobber them. A scramble is not graceful; people scramble when they want to get somewhere fast. Also, scrambling refers to altering a message so others can't read it. Putting a message into code is a type of scrambling. Scrambled messages are like scrambled eggs: all mixed up.