This story uses a farm setting to illustrate to children that getting rid of the root of the troublesome weed is a parallel of the root of sin in the heart, as 'the weed with an ill name'. 
"God may also be represented as having prepared the field of our hearts, and put good seed into them, and requiring us to take care of this good seed when it springs up, and to keep under the weeds which would choke the tender plants and destroy them", being an analogy to the Parable of the Good Sower.