Actually, the rhetorical device is a simile, not a metaphor. A metaphor is an equivocation of two unlike things. In a metaphor, one concept/thing represents or takes the place of another (e.g. "the floodgates of my mind" -- "floodgates" operates as a metaphor for the parts of the mind responsible for repressing memories).
A simile, unlike a metaphor, is a comparison of two unlike things. It's also usually accompanied by the words "like" or "as". In this case, the author compares the children's faces to rootless weeds to suggest that their appearance has been disturbed somehow, much like any plant that's been uprooted (can't make an educated guess as to what exactly happened without more context).