The answer that Menachem gaveMenachem gave is brought up by Rashi on the pasuk. The question still remains, what did he thought he would achieve by running away? This reminds me of the situation in which Moshe Rabenu told Hashem, Shemot 32:32, that if you don't pardon Am Yisrael "omit me" from your book. Out of love to Am Yisrael he didn't want to be part of the punishment. Same here: Yonah, out of love to Am Yisrael, doesn't want to be part of disgracing Am Yisrael, so he uses his Bechira chofshit (free will?) and prefers to die and not be part of the plot.