The commentators explain that the purification process is all about infusing the metzora with a sense of humility. The cedar wood represents his arrogant nature prior to his sin, with the crimson thread (crimson is the product of a dye taken from a lowly worm), hyssop, a lowly bush, atoning for his previous haughtiness (when these substances are dipped into the blood of the birds). Horav Shimon Schwab, zl (cited by his son in Rav Schwab on Chumash), suggests that these three items: cedar wood, crimson thread and hyssop represent three types of people who need to focus on the lessons of humility.
A Jew who has very little spiritual capital, who has not learned, who has not performed good deeds, and whose davening is equally deficient has very little – if anything – about which to be arrogant. He is likened to the lowly hyssop that has no value.
A Jew who has learned Torah, performed good deeds and davens as a Jew should – but acknowledges that he has sinned – is far from perfect. He is to be compared to the pure white wool that is stained crimson by the worm’s blood. He is substance that has been besmirched (a victim of relying on his laurels and perhaps not doing enough).
The third person requires a different lesson in humility. He is a person of true stature, a talmid chacham, Torah scholar, who has major spiritual achievements in his repertoire. Furthermore, he has not sinned. He, too, must humble himself like the eitz erez, a branch (of cedar wood) taken from cedar tree. In comparison to the truly great people that preceded him, he is but a branch of a large tribe, a twig– a sampling from a large, powerful tree. He, therefore, has very little reason for pride.
