Since body of lord Krishna is meghshyam & glittering like rainbow the color of Dhwajaji is also Saptarangi like rainbow. These red, green, yellow, blue, white, pink and saffron colours of Dhwajaji have significance.
RED: It is used for good occasions. It indicate bravery, it becomes source of inspiration to person who is getting one dhwaja flurrying only.
GREEN: It is symbol of peace & progress entire universe is spread by green color in mountains, fields, garden in form of trees, leaves, crop etc. It has capacity to increase mental strength of human being. Ancient rushis were living in ashrams surrounded by greenery for that reason only.
YELLOW: It is symbol of knowledge. It also symbolizes integrity & prompt human being for more knowledge. Yellow pitamber of lord Vishnu symbolize his immense knowledge, lord Krishna & lord Ganpatiji also wear yellow pitamber. Both remove poverty of their devotee & glue them prosperity hence both are worshiped.
BLUE: It is symbol of strength. Almighty has sparingly spreaded blue sky above us & blue sea beneath us Bhagvan Vishnu & goddess Laxmi resides in sea bath in Ganga & Yamuna is considered most pious it further indicates inner strength of person who can control his desire & organs effectively. Balramji was having this quality.
WHITE: It symbolizes peace, piousness & cleanliness. It is formed by mixing seven colors. It indicates cleanliness of mental & physical state.
SAFFRON: It symbolizes bravery. When there is increase of dishonesty, mal practice & injustice, this color prompt to fight against it.
PINK: It symbolizes joyfulness. Example is rose flower, Rose flower remains between thorns it shows that mankind should keep their life delicate like rose but should also take thorn like tough ness when occasion demand.
Thus all colors of dhwaja indicate different characteristics which are beneficial for better life.