Why Does Quran say that Jews Worship Ezra (Uzayr) as God's Son?

The statement of Allah ﷻ that “AND THE JEWS say, "Ezra is God's son," while the Christians say: "The Christ is God's son"”[1], does not in any way mean that Allah ﷻ is generalizing this crime for all Jews and this can be clearly understood by the fact if one reads the prior and subsequent verses that follow it. If one carefully reads Al Quran 9:30 along with verses that follow and precede it, it is quite noticeable that Allah ﷻ is declaring a list of crimes that various disbelievers (kafirs) among the Jews and Christians commit against their own religious teachings including war like aggression:

“Fight those of the People of the Book (i.e. Jews or Christians) who do not [truly] believe in God and the Last Day, who do not forbid what God and His Messenger (i.e. Moses or Jesus) have forbidden, who do not obey the rule of justice, until they pay the tax and agree to submit. The Jews said, ‘Ezra is the son of God,’ and the Christians said, ‘The Messiah is the son of God’: they said this with their own mouths, repeating what earlier disbelievers had said. May God confound them! How far astray they have been led! They take their rabbis and their monks as lords, as well as Christ, the son of Mary. But they were commanded to serve only one God: there is no god but Him; He is far above whatever they set up as His partners!……..Believers, many rabbis and monks wrongfully consume people’s possessions and turn people away from God’s path. [Prophet], tell those who hoard gold and silver instead of giving in God’s cause that they will have a grievous punishment.”[2]

These verses were revealed when the Prophet ﷺ was preparing to face Byzantine Christian (Roman) forces at Tabuk. Just by observing the words “Fight those of the people of the book (i.e. Jews and Christians)” is sufficient to realize that the entire context is addressing crimes of certain members of Jews and Christians and not all. It mentions the following list of crimes committed by certain individuals from these 2 communities:

1. They do not truly believe in God and their accountability before Him on judgment day.
2. Do not forbid what their own messengers have clearly forbidden.
3. Do not obey the rules and respect justice.
4. They also say so and so is the son of God (Jesus or Ezra)
5. They take their Rabbis and Monks as Lord i.e. they follow their word even if it contradicts the clear teachings of God in their books thus bringing them at par with God.
6. Many of them even wrongfully consume people’s wealth and turn people away from God i.e. due to the greed of their religious leaders people don’t follow them and abandon the path to God.

It’s quite evident that all of the above is not committed by each and every Jew and Christian because Quran explicitly mentions the good and believers among them elsewhere and would contradict itself if understood in this manner. Therefore the words “Jews said ‘Ezra is the son of God’” is a crime of idolatry, one of the grave ones that Quran attributes to some of the Jewish community members as evidence suggests some of them did commit at the time of the Prophet ﷺ. We also need to keep in mind that Jews, all of them do not follow same thought, there are various sects and groups that have existed in the past and still exist. Some have survived down to our times while others perished in history. It is noted in classical Quran commentaries such as Tafsir Tabari in which according to a Tradition on the authority of Ibn Abbas (r.a) some of the Jews of Madinah once said to Prophet Muhammad ﷺ: “How could we follow you when you has forsaken our qiblah (prayer direction) and do not consider Ezra a son of God?”[3] According to another hadith source these 4 Jews who came to the Prophet were namely: Salam ibn Mushakam, Nu'man ibn Ufay, Shaas ibn Qays and Malik ibn Summer.[4]

Therefore there is historical background and evidence that when this verse was revealed there were a group of Jews who held the belief of Ezra or Uzayr (alaihi salaam) being a son of God. Thus among the many listed crimes that Allah ﷻ charges members of these 2 communities the crime of idolatry was indeed committed by some Jews in Madinah. It could very well be that there is a sect of Jews that still holds that exact belief or a belief that venerates Uzair (alaihi salaam) (Ezra) to such a high degree that entails divinity. And Allah ﷻ knows best.

References:
[1] Al Quran 9:30
[2] Al Quran 9:29-34
[3] Muhammad Assad - Message of the Quran - Surah Taubah pg 364
[4] Tafsir Al Baghawi http://islamport.com/l/tfs/799/1238.htm