The controversy seems to center mostly on the section of his talk described like this by the Journal World:
Miller said the root of the portrayal of religion and evolution as opposites may come from scientists who have an “anti-theistic interpretation of evolution,” a stance he disagrees with.
“People of faith are shooting at the wrong target. They should not be shooting at evolution itself,” he said.
Miller, a Catholic, said evolution has been remarkably robust in answering criticism through fossil records, the fusing of human chromosomes and other examples.
Instead of attacking evolutionary theory, the argument should be against the anti-theistic interpretation of evolution, he said.
As Dr. Myers agrees, “Miller is not trying to redirect creationists to fight atheists, and he’s very clear that all of us need to stand together in our opposition to bad science.” I think that was fairly clear from what he said, but I don’t blame Dr. Myers for raising a ruckus.