Atheism leaves too much room for error.

[Tiberius]

Look, I'll sort this out for you. Here is the quotation:

Through faith we understand that the worlds were framed by the word of God, so that things which are seen were not made of things which do appear.

Note the first part of the sentence "the worlds were framed by the word of God". This is important for the rest of the sentence to be in context. It simply means that everything was made by something that does not appear (i.e. God, or God's "word").

The whole statement is a reference to the ethereal nature of God; that everything was made by him even though he does not manifest himself as physical.

Nowhere does the statement mention atoms or anything to do with atoms.