Answer: God disciplines us because He loves us, and He punishes everyone He accepts as a son, (verse 6); and He disciplines us for our good, that we may share in His holiness, (verse 10). This discipline produces a harvest of righteousness and peace for those who have been trained by it, (verse 11).
MORE INFORMATION AND/OR OTHER SCRIPTURE REFERENCES:
God's great love includes a constant vigilance on our behalf--a combination of loving kindness in guiding us, and the discipline of hardship and suffering so that He might educate His children. Thus, in the case of the Christian, suffering is God's educational process by which he is fitted to share God's holiness (verse 10). It is a necessary element in the Father-child relationship:
Proverbs 3:11-12: "My son, do not despise the Lord's discipline and do not resent His rebuke, because the Lord disciplines those He loves, as a father the son he delights in."
Revelation 3:19-20: "Those whom I love I rebuke and discipline. So be earnest, and repent. Here I am! I stand at the door and knock. If anyone hears My voice and opens the door, I will come in and eat with him, and he with Me."
There is also a sternness--a justice--in punishing us (the word "punish" literally means "to flog") when we need and deserve the punishment so that our faults may be corrected. It is a hard lesson for God's children to learn and to understand. The proper response of a child of the Father to His discipline is given in verse 9: "submit to the Father of our spirits and live!" Without the submission, there will be sure and certain punishment. If we learn from the punishment, then we will again be the submissive child of God the Father. Just as Christ the Son submitted to His Father in all things, so must we:
Romans 8:5-11: "Those who live according to the sinful nature have their minds set on what that nature desires; but those who live in accordance with the Spirit have their minds set on what the Spirit desires. The mind of sinful man is death, but the mind controlled by the Spirit is life and peace; the sinful mind is hostile to God. It does not submit to God's law, nor can it do so. Those controlled by the sinful nature cannot please God. You, however, are controlled not by the sinful nature but by the Spirit, if the Spirit of God lives in you. And if anyone does not have the Spirit of Christ, he does not belong to Christ. But if Christ is in you, your body is dead because of sin, yet your spirit is alive because of righteousness. And if the Spirit of Him Who raised Jesus from the dead is living in you, He Who raised Christ from the dead will also give life to your mortal bodies through His Spirit, Who lives in you."
We must submit to instruction:
Romans 10:1-4: "Brothers, my heart's desire and prayer to God for the Israelites is that they may be saved. For I can testify about them that they are zealous for God, but their zeal is not based on knowledge. Since they did not know the righteousness that comes from God and sought to establish their own, they did not submit to God's righteousness. Christ is the end of the law so that there may be righteousness for everyone who believes."
We must NOT submit to the basic principles of the world, and to its rules:
Colossians 2:20 through Colossians 3:4: "Since you died with Christ to the basic principles of this world, why, as though you still belonged to it, do you submit to its rules: ‘Do not handle! Do not taste! Do not touch!'? These are all destined to perish with use, because they are based on human commands and teachings. Such regulations indeed have an appearance of wisdom, with their self-imposed worship, their false humility and their harsh treatment of the body, but they lack any value in restraining sensual indulgence. Since, then, you have been raised with Christ, set your hearts on things above, where Christ is seated at the right hand of God. Set your minds on things above, not on earthly things. For you died, and your life is now hidden with Christ in God. When Christ, Who is your life, appears, then you also will appear with Him in glory."
James 4:7: "Submit yourselves, then, to God. Resist the devil, and he will flee from you."
To share in the holiness of the Father, we must be holy. It is a process for those who are made perfect by the blood of Christ, "because by one sacrifice He has made perfect forever those who are being made holy," (Hebrews 10:14). Holiness is a command of the Father, and we have been instructed in it, no longer living in ignorance:
1 Peter 1:13-16: "Therefore, prepare your minds for action; be self-controlled; set your hope fully on the grace to be given you when Jesus Christ is revealed. As obedient children, do not conform to the evil desires you had when you lived in ignorance. But just as He Who called you is holy, so be holy in all you do; for it is written: ‘Be holy, because I am holy.'"
We have been chosen, or called, to be holy:
Ephesians 1:4-6: "For He chose us in Him before the creation of the world to be holy and blameless in His sight. In love He predestined us to be adopted as His sons through Jesus Christ, in accordance with His pleasure and Will--to the praise of His glorious grace, which He has freely given us in the One He loves."
1 Thessalonians 4:7-8: "For God did not call us to be impure, but to live a holy life. Therefore, he who rejects this instruction does not reject man but God, Who gives you His Holy Spirit."
For God's children, who have by practice acquired the capacity of reacting rightly to affliction, there is a "harvest of righteousness and peace." They have submitted to the Father in all things; they persevere through all trials / tribulations / afflictions / sufferings, knowing that God works all for their welfare (or that God works with those who love Him to accomplish good):
Romans 8:28-39: "And we know that in all things God works for the good of those who love Him, who have been called according to His purpose [or, "And we know that God works together with those who love Him (who have been called according to His purpose) to accomplish good"]. For those God foreknew He also predestined to be conformed to the likeness of His Son, that He might be the firstborn among many brothers. And those He predestined, He also called; those He called, He also justified; those He justified, He also glorified. What, then, shall we say in response to this? If God is for us, who can be against us? He Who did not spare His Own Son, but gave Him up for us all--how will He not also, along with Him, graciously give us all things? Who will bring any charge against those whom God has chosen? It is God Who justifies. Who is he that condemns? Christ Jesus, Who died--more than that, Who was raised to life--is at the right hand of God and is also interceding for us. Who shall separate us from the love of Christ? Shall trouble or hardship or persecution or famine or nakedness or danger or sword? As it is written: ‘For Your sake we face death all day long; we are considered as sheep to be slaughtered.' No, in all these things we are more than conquerors through Him Who loved us. For I am convinced that neither death nor life, neither angels nor demons, neither the present nor the future, nor any powers, neither height nor depth, nor anything else in all creation, will be able to separate us from the love of God that is in Christ Jesus our Lord."
Consider the following Scriptures in light of the fact that the discipline of our Father can produce a harvest of righteousness and peace in His dearly loved children:
Psalm 85:10: "Love and faithfulness meet together; righteousness and peace kiss each other."
Isaiah 32:17: "The fruit of righteousness will be peace; the effect of righteousness will be quietness and confidence forever."
Isaiah 48:18: [God said,] "If only you had paid attention to My commands, your peace would have been like a river, your righteousness like the waves of the sea."
Romans 14:17-18: "For the kingdom of God is not a matter of eating and drinking, but of righteousness, peace and joy in the Holy Spirit, because anyone who serves Christ in this way is pleasing to God and approved by men."
2 Timothy 2:22: "Flee the evil desires of youth, and pursue righteousness, faith, love and peace, along with those who call on the Lord out of a pure heart."
James 3:17-18: "But the wisdom that comes from heaven is first of all pure; then peace-loving, considerate, submissive, full of mercy and good fruit, impartial and sincere. Peacemakers who sow in peace raise a harvest of righteousness."