Response to a discussion on this in MennoDiscuss.
I have heard it argued that this parable does not apply to the church, because the field is the "world". However, Jesus often uses the term "world" to mean the broader congregation of Israel (as we see clearly in John 15:19, that "the world" will hate disciples and in 16:2 "the world" casts them from synagogues). Thus, I consider Jesus' use of "the world" to mean the broader people of God, which would today include the church. So I think that today this parable is speaking of the mixed church.
This has an important application for church discipline. The owner tells the workers NOT to pull out the weeds, because they might, by accident, pull out the good plants as well. It seems that Jesus is saying that it is not for us to pull out those who do wrong from our churches. We teach, we train, we make efforts to mature and we protect the immature by showing and doing what is right, warning against the wrong. But who knows when the "evil" one in our midst might not become the one to repent?
It might seem that my interpretation here is in opposition to standard discipline passages such as matt 18, I cor 5, etc. It is not, however. We must discipline those who claim to be full disciples, making it clear to all the congregation what actions are acceptable and what not. However, this discipline is not supposed to be toward ultimate rejection, but ultimate re-acceptance. We need to take Jesus' and Paul's warnings about when we discipline those in the churches that in so doing we do not be judged ourselves. We must be gentle, we must be patient and we must seek the best for the one being disciplined. And, most of all, we must accept them at the first sign of repentance. After all, it is what God does for us.