The Bible doesn't state where Jonah was when God called him to go to Ninevah, but it does specify that he went down to Joppa in order to catch a boat to Tarshish. So, according to all the maps I've seen, Jonah must have been somewhere between Joppa and Ninevah. In other words, Joppa was definitely in the opposite direction. Also, from that information, we can glean that Ninevah was not that long of a trip. And we all know that where God guides, He provides. Just ask the missionaries on the mission field or the pastor of the small church or the young woman who left her full-time, paid position to pursue a ministry in writing. Somehow, someway, God always provides.
Now, notice with me what it says in verse three of the above passage: and he found a ship going to Tarshish: so he paid the fare thereof. Hmm, interesting. I have no doubt that God would have made whatever provision Jonah needed to make his trip to Ninevah. Food, shelter, transportation--whatever he needed would have been taken care of. I've seen too many accounts of God providing for His children to believe that Jonah would have gone without. But because Jonah decided to go his own way, which was in the opposite direction of God's will, He had to pay the price.
I've often heard the phrase put this way, "Where God guides, God provides. When you're out of God's will, you foot the bill." Jonah seems to be proof of that. God was not about to fund Jonah's trip to Tarshish. That wasn't where He wanted Jonah, and as we know from the rest of the story, God set Jonah straight. But my point is that, as long as we're in God's will, He will provide what we need. When we're out of His will, we will have to pay the price.
In Jonah's case, I would imagine that the ship fare from Joppa to Tarshish was pricey. After all, he had to cross the entire Mediterranean Sea. That couldn't have been cheap! Similarly, our efforts to go our own way may often cost us a great deal. The question is, are we willing to pay the price? Jonah was, but after a few days in the belly of a whale, he had a change of heart (and probably wished desperately for a change of clothes). Unfortunately, the price had already been paid, and there is no record in the Bible of Jonah getting a refund for his incomplete trip. That's just not the way it works.
Who's paying? Well, it depends on whether or not we're in the will of God. If we are, He'll take care of it. He'll provide as He always has. If we're not in His will, however, we better be prepared to pay a great price for our disobedience. Is it worth it? Well, I'll let Jonah tell you in his own words.
They that observe lying vanities forsake their own mercy. But I will sacrifice unto thee with the voice of thanksgiving; I will pay that that I have vowed. Salvation is of the Lord. - Jonah 2:8-9