That's not an efficient way of thinking about Medieval Christianity, mainly because it was more of a corporate piety and systematic way of understanding the world than the individual secular spirituality that dominates our 21st century belief structures. Being an atheist in Medieval Europe (which is a very broad timeline and geographic area to be analyzing with any single statement) meant that you were rejecting any sense of allegiance to the elites of the feudal hierarchy, who claimed that their earthly authority descended in a celestial-to-temporal hierarchy from God the Father to his human son Christ via the Holy Spirit, and then from Christ to his apostles via his teachings, and then from his apostles to various saints and martyrs via the dissemination and preaching of the Gospels; Medieval European rulers often strove to fit themselves at the end of this divine chain-of-command by associating their history and rule with their great mystical favor with these saints via relics, churches, or lineage.

This is just one of many reasons why being an atheist in the Middle Ages wouldn't have been logical to a Medieval person (e.g. peasants, merchants, craftsmen, etc.): to reject the dogma of Christianity was to reject the systemic power structure that they were living in.

Christianity was thoroughly embedded in the social and political structures of medieval Europe*. The idea of "not partaking" in religion would have been totally foreign to them, as would atheism as a theological stance. Followers of other religions were tolerated to varying degrees depending on the time and place, but mostly had their own societies distinct from the Christian mainstream. Actively trying to avoid practicing any religion would basically require ostracizing yourself entirely.

For an interesting overview of the early middle ages and the role Christianity played in shaping that society, I recommend these lectures. Sadly they cut off around 1000. Still an interesting look at a time period that can be really hard to map modern ideas onto.

* to varying degrees depending on time and place, and with notable exceptions like Muslim Iberia.

Here's a comment I was about to post to a query--deleted as I was writing an answer to it--about whether philosophers would debate with an atheist. Since it is relevant to the overall discussion, an since it's drawn from a nice article by Dorothea Weltecke, I'm going to insert it here anyway:

Medieval philosophy always depended on a theological foundation--"fides quaerens intellectum" or "faith seeking understanding" as Anselm of Canterbury put it in the 12th century. The existence of God was a matter of revealed faith. Dorothea Weltecke addresses the idea of medieval atheism in her article in the new Oxford Handbook of Medieval Christianity (2014). It's worth quoting a passage at length:

"While it was therefore possible to formulate the thought that 'there is no God' and to present it in a theoretical framework, the idea was not taken seriously by theologians or philosophers. Consequently, unlike many other propositions (such as the eternity of the world, or the unity of the soul), the sentence 'there is no God' was never banned from being discussed in the schools. It could be treated as a sophistic assertion of the same quality as the absurd statement that 'the Trojan war was still continuing'; as something so clearly untrue that it did not threaten faith. In this context Siger of Brabant . . . presented the idea 'there is no God' in his so-called Impossibilia, intended for the training of students in logical disputation. Only one medieval scholar addressed the thought that there is no God as a theological error and developed a more lengthy answer. William Peraldus (d. 1271) treated it as an utterly foolish proposition, quoting Psalm 13 and 52 ('the fool says in his heart, there is no God') and an already long tradition of commentary literature. For Peraldus, those who believed such a proposition were not even worthy of punishment. They needed brains instead of beatings."

EDIT: Let me also mention John H. Arnold's Belief and Unbelief in Medieval Europe (2005), which is the most thorough investigation of medieval agnosticism, where he suggests that, as hazy as the evidence is, there are suggestions that ordinary people here and there did occasionally slip into a deep skepticism or outright doubt about religious matters, but that this was not terribly troubling since "there was no one medieval lay faith but a spectrum of faith, belief, and doubt." On a practical level, what mattered was your contribution to your group, not how odd your beliefs might be, or as Arnold puts it, "A man lives well, works hard, plays his communal role--what then matters his beliefs?"

Worth noting: the following is mostly about what we would now think of as the Catholic world. Medieval Europe was also a big place and covering a wide time period, so generalizing is hazardous. Also, I'm a little out of it today, so my prose may be a little stilted or unclear.

Depends what you think makes someone religious, and what standard one really needed to uphold to be considered as partaking in organized religion. Was it about adhering to the word of the Pope, or about the participation in church or religious life, or dogma and Christ?

In general, people were aware that many of the activities of the organized church were farcical when considering its supposed role in shepherding the faithful. Especially by the time you get to the schisms of the later middle ages, the bald plays for power and money by Church leadership, both in international politics and at the local level, resulted in anger towards them.

You can find references to specific historical leaders being religious or being disinterested. Some nobles were considered pious and noted for their modesty, faithfulness to their wives and constant prayer, while others were noted as lecherous and disinterested in prayer. The Pope was such a big part of the political landscape, however, that I don't think many major nobles would have totally disregarded religion; many of those who were disinterested in religion would pay lip service (and/or give funds) to religion and religious institutions. A common practice would be a payment to endow a prayer on behalf of one's soul by a group of monks, even by the plainly irreligious.

The Pope's place in the political landscape, and position as a ruler of territory, also meant that he was involved with negotiations, alliances and treachery just the same as any other king in Europe, and the popes were not treated with any kid gloves or due reverence by any of his counterpart heads of state.

Within the third estate, it's hard to make generalizations with total confidence. There was certainly a spectrum of reverence for the church, and there are many noted instances of the church being openly mocked, but it was the Church on earth being mocked rather than religion itself. There was cathartic anger at the establishment, but the practices involved in belief were still followed, by and large.

It's also relevant to remember that there were those who rebelled against what existed of organized religion while still acting as believers, and these individuals and groups were condemned as strongly as anyone who simply didn't practice because of their statuses as threats to the primacy (and political relevancy) of the church. John Wycliffe and his followers, the Lollards, are a prime example of this.

Though no examples are coming to mind, I am sure I've read about people who openly disregarded religion and the religious leadership entirely.

So say you had a time machine and went back to 1100 AD England and decided to just live out in the woods. You bough your land off the local lord or whoever happens to own it and just live day to day farming and hunting. Would the community come after you for not showing up to church?