Why did Yonah flee?
Rashi (from Mechilta, Hakdamas Bo): He thought, if I tell them and they repent, I obligate Yisrael, who do not heed the Nevi'im's words! Radak ? he knew that Goyim are close to doing Teshuvah.
Malbim (2): He understood that his mission will be bad for Yisrael ? it will show that Ashur has more merit than Yisrael, and they are worthy to afflict Yisrael. He preferred to kill himself at sea than to case evil to Yisrael. Mahari said, this is why the Mechilta (Bo) says that he put the son's honor over the Father's honor; he gave his life for Yisrael. Also refer to 1:2:1:3.
Malbim: Until now, Hashem merely commanded him to rebuke them. He feared lest Hashem give to him a Nevu'ah to tell them, and then he will be forced to go 1 .
Malbim explained (2) that also now, an Aseh obligated him to go, just if he will be given a Nevu'ah to tell, the punishment for refraining will be greater (Chayav Misah). (PF)
Where is Tarshish?
Rashi: There is a sea called Tarshish in Chutz la'Aretz.
How did he think that he can flee from Hashem?! David said "v'Ana Mipanecha Evrach" (Tehilim 139:7)!
Rashi (from Mechilta, Hakdamas Bo): The Shechinah does not dwell in Chutz la'Aretz 1 . Hashem said, I have messengers like you to send after you and bring you! A Mashal for this is a Kohen's slave who fled to a cemetery. His master said, I have slaves like you to send after you and bring you from there! Radak citing Chazal ? one who flees, he flees to where he can stay. Does one flee to one who fled?! The sea fled Me ? "ha'Yam Ra'ah va'Yanus" (Tehilim 114:3), and you fled to the sea7!
Radak: The Navi was full of Chachmah. He intended to flee from Ru'ach of Nevu'ah. He thought that Ru'ach Nevu'ah will not dwell on him in Chutz la'Aretz. Targum Yonasan is [he fled] from prophesizing in the name of Hashem.
Malbim: Sometimes Nevu'ah comes in Chutz la'Aretz after one had it in Eretz Yisrael, e.g. Yechezkel. Yonah did not flee to a Midbar, for we find that Eliyahu fled to a Midbar (Chorev) in Chutz la'Aretz and saw Divine visions. He thought that Ru'ach Hashem will not come upon him on a boat, for on the sea one's mind is not settled due to the pain of sailing, or because he will be among idolaters. He intended "Lavo Imahem" ? in their company.
Malbim citing Mahari: 'Mipnei Hashem' refers to His knowledge and Hashgachah ? one cannot flee from this! 'Lifnei Hashem' refers to clinging to Him and the Shechinah dwelling on him. This does not happen in Chutz la'Aretz, so Hashem will not send Nevu'ah to him there.
From where did he descend to Yafo?
Megilah 15a: If the verse tells a Navi's city, he was from there; if not, he was from Yerushalayim. (Radak is unsure, for here it does not name his city, but it names it in Melachim II, 14:25. ? PF)
What is the meaning of "Ba'ah Sarshish"?
Radak: It was ready to go to Tarshish.
What do we learn from "va'Yiten Secharah"?
Rashi citing Nedarim 38a: He paid the hire of the entire ship 1 . Radak, Malbim ? this was so it would go soon, and not wait for merchants and merchandise; he wanted to flee quickly 2 . The Gemara learned from here that Nevu'ah comes only on an Ashir.
Rashi: He paid for the voyage in advance 3 . Normally, people do not pay until the ship embarks.
Why does it say "va'Yered Bah"?
Radak: One who embarks in the sea is called Yored ? "Yoredei ha'Yam ba'Aniyos" (Tehilim 107:13). The seashore is lower than the rest of the dry land.
Radak citing his father: The boat is deep. He descended into it. It says also "Yarad El Yarkesei ha'Sefinah" (5).