In this post I am not giving an in-depth exegesis of Hebrews 12:3-11. I am simply putting down some principles from the passage without defending them.  Here is the passage (ESV):

Consider him who endured from sinners such hostility against himself, so that you may not grow weary or fainthearted. In your struggle against sin you have not yet resisted to the point of shedding your blood. And have you forgotten the exhortation that addresses you as sons? “My son, do not regard lightly the discipline of the Lord, nor be weary when reproved by him. For the Lord disciplines the one he loves, and chastises every son whom he receives.” It is for discipline that you have to endure. God is treating you as sons. For what son is there whom his father does not discipline? If you are left without discipline, in which all have participated, then you are illegitimate children and not sons.

Besides this, we have had earthly fathers who disciplined us and we respected them. Shall we not much more be subject to the Father of spirits and live? For they disciplined us for a short time as it seemed best to them, but he disciplines us for our good, that we may share his holiness. For the moment all discipline seems painful rather than pleasant, but later it yields the peaceful fruit of righteousness to those who have been trained by it.

1. God is sovereign over all that happens to us including our suffering.  He brings suffering, hardship, persecution into our lives. It does not just happen to us. The writer of Hebrews is talking to people who have undergone some persecution (10:34) and will probably undergo more. The author puts this persecution in the context of discipline by God.
2. God disciplines us because of indwelling sin. But there is not normally a one to one correlation. Usually we can’t say, “My tire went flat because I yelled at my kids.” But we can say, “I am a sinner. God is rooting out that sin by making my tire go flat.” Remember the goal is not to escape the hardship necessarily though you can and often should do that. I am not encouraging a refusal to take medicine or to stay in an abusive situation any more than a man would refuse to fix a flat tire. What I am saying is that in all these situations one of God’s purposes is to kill sin and cultivate holiness in us.
3. God’s discipline includes all the things big or small he brings into our lives to point out sin and press us to holiness. Daily hardships such as marital strife, difficulties with children, conflict at work, or physical sickness are all part of God’s “training” us in righteousness.
4. His discipline can be something as simple as a rebuke from a friend or a sermon. But it can also be more severe than that. In Hebrews 12:6 the word translated “chastises” in the ESV is translated “scourges” in the New King James. The latter is the better translation. The word is used in the crucifixion accounts of Christ being flogged. Sometimes God’s discipline can resemble a flogging.
5. God’s discipline, the hardships, difficulties, and rebukes he brings into our lives are not a sign that he has left us, but rather that he has drawn near. Discipline is a sign of God’s love, delight, and acceptance of us.  We are sons so we are disciplined.  We must remember this truth when we face hardships.
6. A professing Christian whom God does not discipline or rebuke is someone God has left to his own devices. He is an outcast and has been disinherited. The line here is difficult. But many apostate Christians and non-Christians seem to lead easier lives than those who follow after Christ (Psalm 73:4-12).  One reason for this is that God is not training them.
7. God’s discipline is always perfectly suited to each of his children.  An earthly father disciplines as “seems best to him.” Sometimes he gets it right. Other times he gets it wrong. That is never the case with God. His discipline is perfect in scope, timing, method, and severity. Whatever he is doing in our lives is perfectly calculated to train us in godliness.
8. God’s goal in disciplining us is our holiness (12:10). He does not strike us to destroy us, but rather to deliver us from the sin which remains in us. The goodness of God must remain firmly fixed in our minds if we are to profit from his discipline. His discipline brings life.
9. Discipline is unpleasant and painful when we are receiving. However, the point of the passage is that we look beyond the immediate pain to future fruit. Much of the Christian life is learning to push through present pain in faith as we look to the future reward (c.f. 11:7, 12, 16, 26).
10. Finally discipline is only profitable if we do not despise or become discouraged by it, but instead we are trained by it. To despise means we spit on it. We reject and hate it. This comes either from forgetting that God is good. We see him as hurting and harming us. Or it comes from our desire to cling to our sin. We don’t want to be holy so we spit on the process necessary to get us there. The other option is that we become discourage by it. We can’t see that God will sustain us as he disciplines us. Or we don’t surround ourselves with the necessary support to run the race. Discouragement is a danger in the Christian life. We will only be trained by God’s discipline if we believe God does it out of love for us, for our good, and that he will keep us in the midst of it.