Why do we think God created the Universe from nothing...

if Genesis 1:1 does not describe creation ex nihilo but simply bringing order out of pre-existing chaos?

Because creation ex nihilo seems to be described in other places.

John 1:1-3

In the beginning was the Word, and the Word was with God, and the Word was God.  He was in the beginning with God.  All things came into being through Him, and apart from Him nothing came into being that has come into being.

Colossians 1:15-17

 He is the image of the invisible God, the firstborn of all creation.  For by Him all things were created, both in the heavens and on earth, visible and invisible, whether thrones or dominions or rulers or authorities--all things have been created through Him and for Him.  He is before all things, and in Him all things hold together.

Of course, for the Colossians passage you can argue that the creation being described is all about the social order and not physical things.  Still, there are way more verses that have implications for creation found throughout the Bible than Genesis 1.  So maybe we have to rely on tradition and philosophy over sola scriptura for an ex nihilo doctrine.