What does it mean for God to discipline us?

First of all, it means God loves the one whom he is disciplining (Hebrews 12:6). 

Second, it means that God is working correction into the person whom he loves. If you've been a Christian for any length of time, you have probably experienced the discipline of God. It can be very strong or it can be very gentle. Either way, it is the loving grace of God to be disciplined by him.

Sometimes God communicates to us via scripture where he enlightens the word of God to our hearts and our minds and brings us to the place of confrontation with our sin. 

Other times, God uses events that are out of the ordinary. They are too "coincidental" to be coincidental. In these times, God is getting our attention. 

The Father of Spirits

 "Furthermore we have had fathers of our flesh which corrected us, and we gave them reverence: shall we not much rather be in subjection unto the Father of spirits, and live?" (Hebrews 12:9)

Human parents transmit physical characteristics to their offspring, but our spiritual attributes come from God, for He is "the Father of spirits." Paul recognized that all men are "the offspring of God" (Acts 17:29), and that each man is still "the image and glory of God" (1 Corinthians 11:7).

Thus our spirit/soul nature, as distinct from our body of physical/mental flesh, has come from God, who created it and united it with our body, evidently at the moment of physical conception in the womb. It is obvious that the "image of God," man's spirit/soul nature, could not be transmitted genetically via the "genetic code" and the DNA molecules, for these are simply complex chemicals programmed to transmit only the physical and mental attributes of the ancestors to the children.