[9.30] And the Jews say: Uzair [Ezra} is the son of Allah; and the Christians say: The Messiah is the son of Allah; these are merely verbal assertions in imitation of the sayings of those who preceded them; may Allah ruin them; how do they turn away from the truth!
[9.31] They have taken their rabbis and their monks for lords besides Allah, and (also) the Messiah son of Marium and they were enjoined that they should serve one God only, there is no god but He; far from His glory be what they set up (with Him).
What Quran is suggesting is that calling somebody a “son of God” is simply a phrase which Jews and Christians have adopted from earlier polytheistic religions, which signifies nothing. So if some Jews in Arabia had given Ezra the title “son of God,” in the same manner that Ephraim, Jacob, David and Solomon had been called “son of God” in the Torah, they shouldn’t do that as the term itself is reminiscent of polytheistic beliefs. If you read the next verse, God accuses both Christians and Jews of treating or relying on their priests as if they are gods. God is not saying that all Jews CONSIDER Ezra “son of God;” He is simply opposed to the term, regardless of how Jews in Arabia interpreted it. In other words, Jews and Christians should not use such terminology, as it is false, and not let their priests override the word of God with their own opinions. Note that in verse 9:31, Jesus is mentioned but not Ezra. The reason is that God knows that Christians take the term almost literally whereas that is not the case with Jews.
If you take a look at the work of classical Islamic exegetes, this issue has been commented upon. Allow me to quote from a recent two-volume book called “Sirat al-Nabi and the Orientalists,” which is a thorough rebuttal to all the charges that have been leveled by Christian/Jewish authors against Islam:
“Of course there is no evidence in the extant Old Testament about it; but the Quran was not referring to what is written in the Old Testament about Uzayr but to the belief and assertion of some Jews of the time who regarded Uzayr as the son of God. In fact the ayah [verse] in question starts with the expression “And the Jews say.” The commentator Al-Baydawi…makes it clear with reference to this ayah that because the Old Testament was given its present form by Uzayr, many of the Jews considered him a “son of God” and that specially at Madina there was a group of Jews who held that belief…Not only Al-Baydawi but also other commentators mention that the ayah refers to the views of a particular group of the Jews. For instance Al-Tabari gives a number of reports together with their narrators specifically mentioning the leading Jews of Madina who considered Uzayr a son of God. The most prominent of those Jews were Finhas, Sullam Ibn Miskham, Numan inb Awfa, Sha’s ibn Qays and Malik ibn al-Sayf. Similarly Al-Qurtubi mentions the same fact and the same names adding that the expression ‘the Jews’ occurring at the beginning of the ayah means ‘some particular Jews,’ just as the expression ‘people told them’ means not all the people of the world but some particular people. He further says that the Jewish sect who held that Uzayr was God’s son had become extinct by his (Al-Qurtubi’s) time [d. 1273].”
So, as you can read, Muslim exegetes have never stated that the verse in question referred to ALL Jews. And not only is this well documented, even the names of the leaders of Jews who held such views have been carefully preserved in Islamic history books! Muslims have done a remarkable job of recording not only their own history but of other cultures and religions that they came across.
I can just as easily imagine a group of Jews being influenced by Christians and calling somebody they revere a “son of God,” (of course not taking the expression literally).