The 'Atlas' contains a set of fact. Exact reproduction of these facts in the same format would breach copyright (i.e. taking sentence extracts, and re-publishing diagrams etc.).
The company did not originate these facts, so would have pulled them from elsewhere. Quite possibly many other elsewheres.
So, one programmer uses a reference book to obtain public information as a quick and accurate reference to produce software that does something else, not competing with that first product.
This is simply reducing the formatted facts back to simple facts (the database), which could have been garnered from the original sources (or any other source that collected them).
So, if this case were to succeed, it would essentially say that any compiled source of freely available facts could not be used (without payment) to compile another set of facts. If facts could be copyrighted (which they can't) then I'd understand (in law) how they could think of starting a lawsuit up, but as it stands, I can't.
If the author hadn't put attribution to what he thought was a good source of compiled information, instead of doing the job from scratch, nobody would have been any the wiser. He tried to do the honourable thing and place attribution. For his efforts, he gets a set of lawyers on his tail.
Net effect, something good is taken away by someone with nothing to put it its place. Hopefully this story will pass around, getting the company a good old PR kicking for being idiots.