Rashi, whose commentary, unlike other commentaries is obligatory for Jews who fear heaven (see Mishna Brura on 285:2) states the following:
‘You have seen what I have done to Egypt’ – For many transgressions were they liable to receive a punishment from me, before they harmed you, yet I punished them only on your account.
Similarly, if one looks at the Biblical book of Amos, chapter 1, (together with the traditional commentaries) one will see, that although the idolatrous neighbors of the nation of Israel, namely, Dammeseq, Azza, Tzor(Tyre), Edom, and Ammon, were guilty of many sins, nevertheless, the harm that they did to Israel is what sealed their fate.
I would therefore suggest that if one is trying to figure out the supernatural cause for the unusual weather, first look if there have been crimes (in particular, recent crimes) done against the people of Israel and/or the land of Israel.
It is true that in the case of Yona, it was revealed in the end, that it was Yona himself who was the cause of the weather disaster, so of course, issues unrelated to crimes against Israel or the land of Israel could indeed be the cause for the destructive weather. But precedence has to be given to examining the Israel factor.