The flags are more meant to signify culture than nations/states. For me the flags have a cultural relation that's far more powerful than the states. The flags were used by the people as a signifier of culture before the states took them and turned them into their own symbolica. Even in anarchism culture will persist and having symbols for these cultures is important.
Or to put it simply: "The state stole the flag from the people and now we will steal it back by using it to fight against it".