In some way, the fate of the reprobate is part of God’s working all things for the good of his people. If it was not, the all things of 8:28 would not be all things. R.C. Sproul adds, “There is a sense in which even the wickedness of the wicked is redeemed by God to be a blessing to the righteous.” Contemplating this, we could fill a book, maybe many books, with all sorts of reasons for God’s keeping the reprobate around. And, well, God did, already, fill a book on this topic (the Bible). The Scriptures teach, throughout, that God overcomes the evil of his enemies and he works it for the good of his people, by his grace. They go about doing evil; God then overcomes it and works it for good.
A very clear example of this marvel, from the Scriptures, is found in Joseph’s words to his brothers (Gen. 50:20), concerning the evil they did towards him. You may remember how Joseph’s brothers, Jacob’s sons, the patriarchs of the tribes of Israel, sold Joseph into slavery because they were jealous of him. They hated him, so they sold him to some passing Ishmaelites, who then, in turn, took him to Egypt and sold him there. Over the course of events, troubles, blessings, and an interpreted dream, Joseph was raised up by Pharaoh and put in a position to store up grain against a coming famine. Providentially, as a result, his preparations would save Egypt and his family, ironically including his brothers who sold him into slavery. So, it came to pass that, Joseph, forgiving his brothers after his father’s death, said to them:
20 As for you, you meant evil against me, but God meant it for good, to bring it about that many people should be kept alive, as they are today.
Now, the Scriptures make it clear that not only has God called a people to himself for whom he works all things for good, but God also has always allowed vessels of wrath to be intermingled with his vessels of mercy.
We first get a sense of this with Cain and Seth (Gen. 4-5). Also, think of Noah and his family. God mercifully preserved them from his wrath—the flood. Yet, even from that remnant of humanity not all were of good seed. Shem received the blessing; Japheth was blessed to a lesser extent. Yet, Ham, Canaan, was cursed (Gen. 9:25). We see it with Abraham, one man called by God from out of all of humanity. We see this again with Isaac then Jacob, both of whom God chose over their brothers as heirs to the promise. Later in the OT, with the Israelites (God’s holy nation (Ex. 19:6)—“holy” meaning “set apart,” a remnant nation among the nations united by God’s Mosaic covenant), God demonstrates that he always keeps a remnant for himself, even when the nation, overall, had gone over to evil in violation of the covenant.
We’ve been churning through the OT historical books for two and a half years now in the evening service. A repeated and constant theme is God’s patience with Israel throughout their history. Those in rebellion against God were exponentially more numerous than those faithful to him. Yet, God, often after letting them suffer for their own folly, kept on saving them. Why? It was for the sake of his remnant, vessels of mercy, according to God’s covenant of grace (e.g. 2 Kings 19:18). The birthing of generations of evil people provided a place for the remnant of God’s people to survive and thrive. Vessels of mercy grew up among the vessels of wrath. God’s Word was preserved by the nation. The seed of the Lord who would one day save the world was protected and nurtured. Despite (with rare exception) evil king after evil king, leading both the northern and southern kingdoms into evil, “the lamp of David” was always before God (at least in Judah – 1 Kgs. 11:36), and God kept his covenant promise to David of an eternal throne (2 Sam. 7). God tolerated the evil reprobate of Israel and Judah so that King Jesus would one day be born and save his chosen people—vessels of mercy.
Why? In order to magnify the riches and glory of his mercy and blessings upon his people.
Jesus, in his parable of the Wheat and the Weeds (Matt. 13:24-30) refers to this same intermingling of the reprobate with the elect within the remnant of his church, which is the continuation of the holy nation (1 Peter 2:9). As Jesus tells the parable, he makes the point that Satan sows weeds into the field where Jesus has already sown his seed (the wheat). James Boice comments,
“In other words, the devil places his own counterfeit Christians among true believers to hinder God’s work…. The devil is going to bring forward people … so much like true Christians, though they are not Christians, that even the servants of God will not be able to tell them apart.” 
This is the reality in which we now live, my friends.