In Jonah 3:4-4:4, Jonah preaches to the Ninevites and they repent. God then relents and has mercy on them. Jonah is furious, and in 4:2 reveals his actual reason for not wanting to come to Ninevah:
And he prayed to the Lord and said, “O Lord, is not this what I said
when I was yet in my country? That is why I made haste to flee to
Tarshish; for I knew that you are a gracious God and merciful, slow to
anger and abounding in steadfast love, and relenting from
disaster.1
Earlier in Jerome's (Eusebius Sophronius Hieronymus) commentary, he says:
Jonah is sent to the gentiles to condemn Israel, because Nineveh had
to repent, but the Israelites still persisted in their
sin.2
Shlomo Yitzchaki (Rashi) has also expressed this idea (that the Israelites would look worse for not repenting if the Ninevites did—which Jonah seems certain they will).
Jerome goes on to say:
And what is more he feared that in spite of his prophesying they would
still not be converted to repent, and that Israel would not be
completely abandoned. For he knew by this Spirit which had entrusted
him with the role of hero among the gentiles, that once the nations
had come together in belief, then Israel would surely perish. And he
feared that whatever was to happen in the future would not happen in
his time.3
According to Jerome, Jonah had Deuteronomy 32:21 in mind (which Jerome considers the repentance of the Ninevites to be a fulfillment of):4
They have made me jealous with what is no god; they have provoked me
to anger with their idols. So I will make them jealous with those who
are no people; I will provoke them to anger with a foolish nation
(ESV).
Jerome clarifies his position later in his commentary:
[Jonah] shows the signs of his suffering and more or less says this:
'I have been the only one of the prophets chosen to announce my
people's ruin to them through the safety of others.' Thus he is not
sad that the crowd of gentiles should be saved, as some people
believe, but it is the destruction of Israel....
...[Jonah] replies with assurance, 'I do well to be angry and to
suffer even unto death. I did not want to save one only to see the
others perish, to gain foreigners only to lose my own'.5
Isaac Abarbanel supports this idea,6 speculating that if Ninevah did not repent, God wouldn't allow them to become powerful enough to destroy Israel. But if they did repent (and Jonah clearly suspected that this would be the case), they would once again become a world power and cause the destruction of (what remained of) the Northern Kingdom of Israel.
So to clearly answer the question, Jonah may have believed that the repentance of the Ninevites would cause God to spare them from destruction. And since Jonah viewed them as a threat to his own people, he feared that if they were spared, it would mean the destruction and exile of the Israelites at the hands of the Ninevites. I have demonstrated this interpretive option both in Jerome's own writings (the same work cited in the question) and in those of other Hebrew Bible scholars.
1 Jonah 4:2, ESV.
2 Jerome, Commentary on Jonah, translated by Robin MacGregor, retrieved from Litteral's Christian Library, 1:1-2.
3 Ibid., 1:3.
4 Ibid., 4:1.
5 Ibid., 4:1, 9. Jerome sees Ninevah as a 'prefigure' of the Christian Church, with this incident being a prophetic historical event predicting the expansion of the kingdom of God in Christ by the 'grafting in' of the Gentiles.
6 According to Steven Bob in Go to Nineveh: Medieval Jewish Commentaries to the Book of Jonah, Translated and Explained, Isaac Abarbanel points out that for Jonah, ensuring God’s destruction of Nineveh, the capital of Assyria, by refusing to prophesy, would prevent Israel's destruction by Assyria's hand. Jonah is willing to forfeit his life in the exchange, making his leap into the sea a heroic act on behalf of the Jewish people rather than a cowardly or naive attempt at fleeing God's presence.
