Exodus 20:5-6 (also Dt 5:9)
I, the LORD your God, am a jealous God, punishing the children for the sin of the fathers to the third and fourth generation of those who hate me, but showing love to a thousand generations of those who love me and keep my commandments.
Fathers shall not be put to death for their children, nor children put to death for their fathers; each is to die for his own sin.
The soul who sins is the one who will die. The son will not share the guilt of the father, nor will the father share the guilt of the son. The righteousness of the righteous man will be credited to him, and the wickedness of the wicked will be charged against him.
Matthew 23:35 (also Lk 11:50-51)
And so upon you will come all the righteous blood that has been shed on earth, from the blood of righteous Abel to the blood of Zechariah son of Berekiah, whom you murdered between the temple and the altar.
I think these passages can be understood by looking at what God does in the Bible. When parents do wrong or experience punishment on earth, their children share the ill effects - if a parent is put in jail, their children are adversely affected; if a parent is abusive or negligent, their children suffer. This sort of thing occurs in many places in the Bible. For instance, Achan and his family died as a result of his disobeying God (Joshua 7). However, while children often shared the earthly punishment of their parents, they would not be punished for their parents' sins in the afterlife. Ezekiel 18 makes it clear that the real guilt belongs to the person who sinned, not their family. Deuteronomy 24:16 is an application of this principle to human-administered justice: while God decreed that some sins merited the death penalty, humans were not to apply the penalty to anyone other than the guilty party. If, as in the case of Achan, a family or nation was to be corporately punished, only God had the authority to decide that corporate punishment was merited.
On the other hand, God often extends mercy to the families of people who are righteous. Rahab's family was allowed to survive because she respected God (Joshua 2). God spared Noah's family because Noah was righteous (Genesis 7:1). And of course the nation of Israel was blessed because of Abraham's obedience to God (Genesis 22:17-18). Again, the blessings received by a righteous person's family only affected their life on earth. A person's relatives will not be saved or condemned in the afterlife because of that person's actions; rather each will be judged as individuals.
In other words, the true distinction is between life on earth and the afterlife. People do not receive precisely what they deserve while they are on earth; they are affected by the actions of those around them, and thus can be said to be punished (i.e. experience suffering) for their relatives' wrongs. But this is a temporary state of affairs; when people enter the eternal afterlife, they will be judged as individuals, and what punishment they receive will be only for things they are truly guilty of.
Why then would God corporately punish a family when not all of them had sinned? In some cases, the relatives of the wrongdoers shared in their guilt by failing to stop the person from doing wrong or rebuke them for their wrong. In other cases, it's possible that the loss of the wrongdoer's family line was part of their punishment.
Finally, what about the passages in Matthew and Luke, which seem to say the Jews of Jesus' day would be held accountable for murders committed by previous generations? Jesus' statement is true in a figurative sense, i.e. that his contemporaries who rejected him would experience a far greater condemnation than others who rejected him without the benefit of hearing his teaching or seeing his miracles. The Jewish leaders were expected to know the Scriptures and be in close relationship with God, both of which would have enabled them to recognize Jesus as the Messiah. They were given advance notice of the Messiah's arrival by John the Baptist. They also had many opportunities to hear Jesus' teaching, interact with him and witness the miracles he performed, especially since Jesus focused his ministry on the Jews. Since they had far more opportunity to accept Jesus than anyone else, their punishment for rejecting him would be far greater than that of others (see also Degrees of punishment in hell).
Jesus' statement can also be taken more literally, in that his contemporaries were guilty of their ancestors' sins to the extent that they condoned their actions and committed similar ones. In fact, they weren't just repeating past sins but were committing ones that were far worse, since the prophet they persecuted was God himself. Considering these two factors, one could make a comparison between the punishment they would receive and the aggregated punishment for all martyrdoms in previous history.
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