In broad, history of ideas-type narratives, historians often characterize epochs like the Enlightenment by means of contrast with the naivete of previous times. The idea is that religious narratives or folklore or whatever had such a totalizing grip on the minds of medieval Europeans that the status of these beliefs couldn't even be questioned. Of course there won't have been a large contingent of atheists, but I find it hard to believe average European Christians were entirely unaware of even the possibility of questioning the truth of religion.
This article by a scholar of the history of atheism covers the basics of why answering this kind of question is so difficult and what we do know about early skeptics and atheists:
http://www.exurbe.com/?p=1824, take a particular look at the paragraph beginning: "“I don’t know,” is the centerpiece here."
To summarize briefly: a 12th century layperson would have a very hard time explaining any of the world without religion. Both ethical and natural philosophy relied heavily on religious explanations. From a modern perspective, we can say "well, why not just accept they didn't know how things worked without relying on religion for everything," but historically it seems early atheism only flourished when atomism was available as an alternative natural philosophy. So, when trying to identify whether someone was an early atheist, whether they knew about atomism is a valuable piece of information.
Could there be 12th century skeptics? There's no way to rule it out. But, they would have to have a remarkably different mindset than the earliest known atheists and have been much more willing to accept their utter ignorance of how the world worked.
Can you explain a little more about what you mean 'religious skepticism'. This could be interpreted, as does /u/j_one_k, in the context of atheism. But I don't know if you mean skepticism of received religion (the Church and its representations in medieval Europe) or actual skepticism about the existence of God. I ask this because in the 11th (and 12th centuries) we have a clearly diffuse sense of how God is constituted in beliefs such that it could seem like an outsider to be nearly a continent of religious diversity, almost polytheist.