You can read
the article for full details, but in a nutshell, the US Department of Justice has filed a statement of interest with the judge that says Google has fallen well short of eliminating the antitrust and copyright concerns. The DOJ points out that the settlement might provide some "public good", but that it falls short of the law in regards to copyright and antitrust.
The DOJ basically said that Google could not have gone to court and somehow come out with this agreement, nor could they even have negotiated this type of agreement over a bargaining table. It looks like the biggest bone of contention is the "opt out" mechanism that Google is demanding. Even though it may result in a "public benefit", it is not something that any party can grant to Google and would require legislative intervention.
Here is the actual
DOJ statement of interest.