They could've been prosecuted, as we know that such people existed by their court records. Mostly when these statements came out of someone's mouth, they weren't exactly being serious. These are cases of blasphemy, which often stemmed from frustration and cursing, often at a tavern drinking or at a gaming table (probably also drinking); but such statements did get people hauled into court.

In 1526, a servant boy in Toledo was brought before the inquisition because he said in a group of people, "I deny God and our fucking Lady, the whore of the cuckolded asshole!" As Alec Ryrie phrases it, these statements are a form of posturing, playing Russian roulette with one's soul by damning oneself to prove that you aren't afraid of anything, or have nothing left to lose. These blasphemy cases are usually men cursing to each other in a male space, people at the time said that women blasphemed less and in different ways. As Ryrie notes, "...typically challenging God's justice or cursing their own births." Oof. Blasphemers denied God but this was a lapse in Christian judgment, there are rarer examples of people who went much further.

In 1448, the Bishop of Worcester was interrogating suspected Lollards in order to root out this heresy, and in doing so recorded the beliefs of a man named Thomas Semer [Seymer?], whose opinions were both entirely his own and completely unlike that of the bishop. Just as Lollards said, he denied transubstantiation. This meant denying the reality of that weekly miracle which only priests could conduct, and thus was denying the very foundation of Christian Catholic organization. But he surely must've shocked the bishop by going further...he said that the soul wasn't immortal, neither heaven nor hell exist, the ritual of Mass was pointless and meaningless, and that Jesus wasn't born from a virgin, of course that's ridiculous! And the Bible? This was only a tool used by the clergy to control the common people. These cynical opinions were the peak of late medieval Christian anti-clericalism, beliefs which did not necessarily deny God's existence but denied those unbelievable lies that corrupt people in power so obviously use to hold onto to their power. But going one step further he gave the bishop some brief version of his real religious opinions: If God and the Devil exist, then the Devil is stronger; perhaps coming to this belief after accepting that evil rules this world. And if we are to have any religion, then paganism is better than Christianity.

Not only a peasant farmer, Thomas was also an idiosyncratic philosopher. He expressed a worldview which still viewed our world as divine, but rejected most of the common ways of understanding divinity; since they were so obviously abused by disingenuous people. And in turning away from the clergy, he embraced the pagan style of religion: a holistic interpretation which accepted the diversity of all human beliefs. All are united in the common goal of praising that divinity. This diversity of belief is to be expected, since these beliefs often cohere with a placed-based belief system - tied to particular natural locations like forests and streams. A system that Thomas must have heard about, as Greco-Romans had their sacred groves with their spirits of the woods and streams, satyrs and nymphs. It isn't coincidental that this is the belief system of someone who could've spent a lot of time reflecting in a quiet place in nature. He knew this was how one accessed divinity, not through accepting the lies of the clergy. He did not repent or deny these beliefs, and was executed.

Thomas Semer was not alone, people before him and after him were influenced by gnosticism: a style of mystic anti-hierarchical Judeo-Christianity which emerged in the early Christian period in Aramaic. These texts continued being read in the Euro-Christian world, surviving underground in book sharing networks (after being translated into Greek and Latin). One belief in gnostic thought is that this world is fundamentally evil, and thus must be ruled by an evil God. This evil God is in fact the Abrahamic one, and while Christianity and Judaism praise this deity and believe themselves to be a true religion, gnostics know better. In the text On the Origin of the World, this malevolent God creates the world and then says, "I am God, and no other exists except me." But when he said these things, he sinned against all of the immortal ones...when Faith saw the impiety of the chief ruler, she was angry...she said, "You err, Samael (The Blind God)..."

Since all paths toward spirituality were acceptable gnosticism was inherently holistic. This radical acceptance was normal in the Roman world in which gnostics lived, as the Roman senator Symmachus said in his 3rd Relation (arguing against institutionalizing Christianity), It is just that all worship should be considered as one. We look on the same stars, the sky is common, the same world surrounds us. What difference does it make by what pains each seeks the truth? We cannot attain to so great a secret by one road... But such acceptance was a dire problem for ancient proto-Orthodox Christians such as Tertullian, whose strict opinions against heretics were supported by later Catholics. Tertullian said, "...[Gnostics] listen equally, they pray equally - even [with] pagans, if any happen to come [to their meetings]...They also share the kiss of peace [a symbol of Christianity] with all who come, for they do not care how differently they treat topics, if they meet together to storm the citadel of the one only truth...All of them are arrogant...all offer you gnosis!"

Gnostic holism extended beyond accepting pagans at their meetings, but in fact the whole cosmos is One and all living beings including ourselves are equally parts of this sacred totality. All dualities are illusory as the Gospel of Phillip says, Light and Darkness, life and death, right and left, are brothers of one another. They are inseparable. Because of this neither are the good good, nor evil evil, nor is life life, nor death death. For this reason each one will dissolve into its earliest origin... and ...in this place [the Other world, at one's death], you see everything and do not see yourself, but in that place you do see yourself - and what you see you shall become.

Late medieval idiosyncratic philosophers read these underground texts and recreated holism in their medieval Christian worldview. In the late 16th century, the miller-heretic Domenico Scandella said (to inquisitors) what at first might appear to be an insult or joke, You might as well go and confess to a tree than to priests and monks. He rails against the corruption of monks and clergy, as Semer did, and this is one interpretation of that statement - What's the point of confessing one's sins to the greatest sinners? But locals told inquisitors that Domenico said other similar statements, and even though these statements are hearsay they do align with his other beliefs: Everything that we see is god, and we are gods...The sky, earth, sea, air, abyss, and hell, all is god. So perhaps it's not simply a joke that we should confess to a tree, since it too is a part of this divine existence it could just as adequately hear a confession as a human.

Domenico did not reject the existence of God, but he rejected so many core principles of Christianity that to his contemporaries he was an atheist. When asked by another man if he believed in the gospels, he plainly replied No I don't. Who do you think makes these gospels if not the priests and monks who have nothing better to do? Domenico didn't know that the man he spoke to wrote down these shocking comments and gave this information to the inquisition. It took years, but eventually inquisitors noticed the similarity between this "anonymous heretic" and Domenico (who had been tried and released years earlier). After this second trial when he was confirmed as a relapsed heretic, he was executed.

AskHistorians has made a podcast about medieval atheism. Not to discourage other in-depth answers here, of course.