JMO, but he would be better described as a Deist, as a lot of Enlightenment philosphers/thinkers were. The modern idea of an atheist didn't really exist at the time and I think it's fair to say there were no or very, very few, atheists back then. At least none who would admit it. This is, after all, a time before Darwin and modern geology and the like.

I haven't finished Leviathan but every reference I recall (and there are lots) suggests that he takes the Bible at its word. He certainly comes off as a secularist and if he had lived in the 19th or even 18th century I would be more surprised if he were a believer than if he were an atheist or agnostic. Given that he favored civil rule over religious -- he questioned the role of religious revelation to individuals with regard to social order, questioning how/why others would accept the individual's (who experienced direct revelation) -- I can see why the church would be wary of him. Care to suggest passages that suggest he was an atheist or agnostic?

He didn’t want to be called an atheist, yet he believed that reality consists only of “matter in motion”. What that means IMO is that he believed in a God made of matter, and that heaven is a physical place.

It’s not a very astute philosophy IMO.