Atheists think they think, but I dont think they do.
No, it's not compatible with polytheism, either. There are a bunch of people who believe in many gods, especially in California.
This decision is not terribly surprising from a purely legal analysis. But it's wrong, simply because the Pledge doesn't establish a religion in violation of the First Amendment. The courts have been moving to a definition which has changed from "no establishment of religion" to "no mention of religion."
This decision was predictable, but wrong. It's going to be overturned, and this is actually going to turn out to be a very good thing in the long run.