This is a good observation! The main issue here is one of interpretation. The Bible has many different genres of literature and thus different parts must be read, interpreted and applied in different ways. I would highly recommend you read this book by Gordon Fee, which explains how to read the Bible according to its different genres. It's free on Google Books.
It is clear that some parts of Scripture are to be taken literally. For example, Jesus' birth, life, death and resurrection, as recorded in the four gospels, are historical facts that should be seen as literal events that happened two thousand years ago. The events described in the letters of Paul should also be taken literally as they did happen during the 1st Century. We cannot that Paul was writing figuratively or poetically. This is like asserting that the reports in the Toronto Star newspaper should be read figuratively as well!
On the other hand, there are texts in the Bible that should be read figuratively. Let me illustrate. When you read poetry like Psalm 95: 4, "In his hand are the depths of the earth..." it is obvious that there is no physical hand of God holding dirt from the Earth's core. This is poetic language and it is because Psalms is a book of poetry. This, however, does not mean we interpret this part of Scripture as untrue. Every figurative piece of language has a literal point. In this case, the psalmist is saying that God created everything, including the Earth, and therefore, it belongs to him. He is the source and sustainer of creation.
That being said, there are still many places in Scripture where it is unclear whether the event is literal or figurative. The classic example is that of Genesis 1, the creation account. Did God literally create the world in 6, 24-hour days? Or should interpret this figuratively (i.e. the point here is God created, and these 6 days could represent thousands, if not millions, or years)? Here is a blog post about how to interpret the creation account.
When it comes to these sorts of controversial texts, we must graciously explore what the Bible says together (meaning that there can and should be healthy debate between Jesus-loving, Bible-believing people on matters like this!). Remember that the goal of interpretation is to find out what God is trying to tell us through the Bible - and apply it to our (private and communal) lives. This is how we ought to read all texts of the Bible, whether the language used points to a literal or figurative event.
[Answered by Pastor HM]
Here is a video of Pastor Tim Keller of New York that explains what we've been talking about briefly
