Consider the daily offerings made to the kami at the kamidana, the household mini-shrine that sits on a shelf high on the wall inside the principal room of the house. The offerings, shinsen, include washed rice, water and salt. People offer these, clap their hands and pray in front of the kamidana. The washed rice symbolizes good health. Water preserves life and cleanses.
Salt is for shiokagen, the act of seasoning food to bring out the flavor.
Salt represents harmony. These three things are essential for people to live satisfactory and useful lives. If people had these, life would be ideal, but this is not the case. Many things prevent people from achieving their full potential. Misogi is efficacious in restoring the natural greatness of soul of which man is capable.