3. That all religion is the same
It’s true, some atheists put all religion into the same category. But most atheists I know have spent enough time around people of different perspectives to know that there’s a huge difference between a snake-handling Pentecostal and a liberal Quaker, not to mention ISIS and the Dalai Lama. I might think they all have the facts wrong, but they are far from equal in theory or practice.
Big differences even exist within one denomination. A progressive Catholic differs from a conservative Catholic on almost every major political and social issue. These differences matter, and atheists who pay attention can and do recognize them instead of painting all religion with a broad brush.