Unlike Marin Luther, who was all too happy to side with the privileged, Thomas Müntzer realised that just reforming the church wasn't enough. He was for real social change and the liberation of the lowest strata of society and wanted to put an end to feudalism.
True atheism should induce the dismantling of social hierachies.
Müntzer was not an atheist (although nothing got done in his era outside the church, so I don't hold that against him). So he's not an examplar of "true atheism" (whatever that even is).
Also, simply dismantling hierarchies without a plan as to what organizational concepts will replace it, is probably not a good idea.
So what I'd say is that "true humanitarians should be motivated to correct injustice and inequality in social constructs."
Perhaps he wasn't an atheist but his ideas were clearly against the church. He closed down the monasteries and fed the needy. He was a militant humanist.
I think it is rather difficult to judge where people like him and Giordano Bruno and Georges Lemaitre were placed on the theistic scale. BUt their acts and achievement certainly set them apart.
@PontifexMarximus I agree. As I said ... nothing got done outside the church so being (at least overtly) an atheist was a non-starter. Indeed, the word "atheist" was just being coined around Müntzer's time (and in France, not Germany), so the framing for the concept was not fully erected yet.