One of the common objections among evangelicals to viewing some parts of the Bible, such as Jonah, as unhistorical, is that such a view is the first step down a long and treacherous slippery slope.
Ken Hamm, a major name in creationist circles, asks "If the Creation and the Deluge stories aren't actual events, as described, then at what point does God start meaning what he says?" Another popular question about Jonah is, if you can't believe in Jonah, how can you believe in Jesus coming back from the dead? Especially when he referred to "the sign of Jonah" as the only evidence his generation would receive of his messiahship! (I'd argue that Jesus' allusion no more requires it to be an historical event than my using the phrase "tilting at windmills" indicates I believe Don Quixote was a real person.)
I believe it was Real Live Preacher who once noted that once people start invoking the slippery slope, they find it harder and harder to use any other sort of argument, until after a brisk slide down, the slippery slope is the only argument they know how to make.
How can I believe in the Resurrection but not in Jonah's misadventure with a marine animal? It's actually pretty easy. I believe the story of Jonah being swallowed by a great fish is a parable about God's love for all nations. I believe that the Resurrection is an actual historical event. (See? It's not hard at all.)
Partly it's recognition that the Bible is a multigenre work. It contains mythology, from Genesis 1-12; it contains folk stories and legends, from Genesis 13-50, the books of Judges and Ruth, and parts of Exodus; it contains history, from Samuel through Kings and Chronicles, plus Ezra, Nehemiah, and Acts; it contains poetry, such as the Psalms and the Song of Songs; it contains wisdom literature, in Proverbs, Koheleth, and Job; mysticism in the gospel of John; theology in most of the Pauline and lesser epistles; personal correspondence such as Philemon; lessons on Christian living, such as the book of James; apocalyptic writing in Daniel and Revelation; and so on. The synoptic gospels actually combine several of these types of writing.
The Bible isn't a history text, though it contains history; it isn't a math text, though it contains some math; and it isn't a science text, though it contains some science. (And some of it appallingly bad, like the way Jacob breeds Laban's flocks so that he can get all the best ones and leave Laban with the weak ones.) I think we do the Scriptures an unncecessary violence when we insist that there is only one way to understand it, and that its every word has to be treated as definitive in terms of science, history. Its only claim about itself is that it's God-breathed and meant for instruction, encouragement, reproof, and revelation.
Given the polyphany of voices in Scripture, I don't think it's unreasonable to regard Jonah as divinely inspired fiction. In what way does that diminish its meaning or message? Either way, its inclusion in the canon shows that God's love abounds even to our enemies, and that his desire is for a broken heart and contrite spirit, rather than to leave a smoldering ruin where a great city once stood.