How common was it in Europe during the medieval ages to not be religious?

I would say 'not very common,' but it depends on how you construe the idea of Religiosity. The culture of Europe (and the Mediterranean) was by and large based around ideas that sprung from religions, Christianity, Judaism, Islam. Everything from the work week to annual holidays formed around religious ideas. Even the church bells told you what time it was. So even if you didn't personally subscribe to whichever belief, the culture was "christian".

As far as the Religion goes, there were always detractors, and there was far more variety of beliefs, interpretations, and practices than one might think. Catholicism in the Middle Ages was nearly always challenged by various reform movements at any given point, backed by individuals both elite and common that felt the status quo wasn't quite right. This ranged from monastic movements which felt the church was missing the mark to heretical movements like the Albigensians that more or less threw out Catholic doctrine altogether. It's likely that relatively few people actually went to church regularly, hence the various reforms of high medieval councils (like Lateran IV) which stipulated that all Christians should, for example, go to confession at least twice a year. In that sense one could say a lack of religiosity was widespread.

If you're wondering about atheism proper, that's a little harder to nail down. There were a few Islamic thinkers and poets, like Al-Razi and Al-Ma'arri who openly mocked religion and expressed what would be the closest thing to "atheism" in their mocking of religion, though they do not declare out right that there is no god. The Goliards, medieval catholic poets, openly mocked catholic religion and the devout and embraced their own "debauched" lifestyle, but never stated that there was no god. Scholastic scholars like Aquinas attempted to use reason to prove God's existence, but it was more of an exercise rather than responding to the postulation that He didn't.