You're reading into the passages from John and Colossians the Church's understanding that was based on 2nd Maccabees. It is the only place the Scriptures speak of God creating out of nothing. The words in John and Colossians translated as "made" or "created" were not technical words indicating creation
ex nihilo, but simply words meaning "made" (or perhaps "brought to pass") and "built", respectively. Nothing in the protestant canon, read "literally" as so many protestants want to read the Scriptures distinguishes between creation
ex nihilo and creation as forming pre-existing amorphous material (as in the creation stories of numerous pagan traditions).
You rightly believe in creation ex nihilo, but it is a doctrine you impose on your short canon of Scripture, rather than derive from it, while for all Christian traditions that existed before the 16th century, it is a Biblical doctrine, precisely because we all (Orthodox, Latin, monophysite and Nestorian alike) have 2nd Maccabees in our canon.