"Lillies that fester smell far worse than weeds."
See Shakespeare’s Sonnet 94. Fitzgerald gives a literary gloss to his belief in rewards for virtue and punishments for not fulfilling your duties (your talents?).
A lily that festers is someone who is talented but did not fulfill their potential, or shirked the responsibilities their talent entailed. Someone like this is worse than someone who is born without talent (a weed), according to Fitzgerald.
To help improve the meaning of these lyrics, visit "Letter to Daughter ("Things to Worry About")" by F. Scott Fitzgerald and leave a comment on the lyrics box