Ramban: Like a father places on his son the yoke of Musar (teaches him ethics) for the son's benefit, ¹ so too, was Hashem chastising Yisrael, with the afflictions of the desert and the test of the Manna, so that they would ultimately appreciate the goodness of Eretz Yisrael and its fruit. ²

Seforno: See answer #1. Just like a father who chastises his son to teach him ethics, Hashem chastises Yisrael (not with the intention of harming them, but) in order to prompt them to attain the level of perfection that He expects of them.

Sha'arei Teshuvah (4:13): It teaches us that Yisrael's difficulties and afflictions are not commensurate with the gravity of ther sins, because Hashem chastises them like a father chastizes his son - a chastizement that stems from mercy. And this is something that Yisrael knows in their hearts.