It seems contradictory that Jesus would condemn one set of weeds while holding up the second as an example. The difference between them seems to be their purpose. The first set of weeds are plants that are pretending to be wheat, yet are growing so close to the wheat that removing them damages the healthy plants. Meanwhile the mustard seed grows into a large bush that birds can turn into a home.
Remembering that all of these parables are descriptions of the kingdom of heaven, I believe that Jesus is warning against those who pretend to be Christians, perhaps going to church and making bold claims about their Christianity. All three parables deal with the growth of the kingdom of heaven, and how such a kingdom can have such humble beginnings. However, He notes that there will be pretenders as well, and that they will not be separated until the final harvest.
Am I a weed that is merely pretending to be worthy of more--hoping to avoid the fire, or am I the weed who grows to provide shelter for others?