Firstly, I think that cynical fits the description very well, secondly I don't think that Atheism fits within the Political-Spiritual Framework of the times.
Indeed, there were actually Atheists, to a certain degree - specifically I remember that an Atheistic sect around India was involved in the Mughal House of Learning, and participated in the Mughal Sultan's infamous religious debates. However, when we look at the Western European Mechanics which all houses and states are build around in CK2, there really isn't a function for Atheism. I like to think of Protestantism as the Secularisation of Christianity, because it detached itself from the Pope, who is sort of seen as the authority of the time, of most of Europe's Christians. It allowed for further secularisation of all things, especially after the Treaty of Westphalia and the diminishment of Monarchies and the role of religion in politics in exchange for a more universal humanist view. Like others who have posted have said, Atheism wasn't a power-player in Medieval times.
Certainly, I'd speculate that it might be like Game of Thrones, where you have a lot of lip-service by the cynical lords, but with evidence of people who are really into their faiths, but I would say that its more like the show Vikings, in how people take their religious values seriously, and their religion in turn determines how they see the world. (If you've seen the show or generally like Historically based drama, re/watch and see the episodes and scenes with Aethelstan who is seduced by both Norse and Catholic faiths, and how he sees the world through those belief systems.)
Lets say you were the King of Bavaria, "Hallo, I am King Hans von Munich"
Now you, my King have decided, "You know what, court of knights, gentry, priests, Papal Ambassador, yes hello Holy Brother, oh and my Court Jew, Samuel, how's it hanging Sam?"
"'The vineyards, my Lord? I written to your Steward, and it seems that the harve-"
"Okay! Great! Very Good, okay, so as I was saying, I was just reading my Bible, which was difficult, mind you because my Father, Hugo the Strong, thought that reading was for snivelling priests, when a real man was out hunting and falconing and learning to ride, anyways, so I've read through the Bible, written down a list of inconsistencies since I was having some doubts beforehand and without asking anyone experienced in matters of faith, I have decided that God is dead. I am no longer a Christian, despite my sons being baptised, they won't be Christians either.
*A priest walks out from the crowd of shocked and muttering nobles and ladies* "My Lord, you would let you and your family be damned by turning to the Godless heathens of the Saracens and Moors and other sons of the devil!?" *he points angrily to Samuel HaYehudi HaChetzar*
"What? No, despite the great strength and ferocity of the Mohammedans and I bet converting would get me some hefty favours with them, I do not believe in god, send this to the four corners of the Kingdom, "God is Dead".
It should perhaps be the right time to explain the Conversions of the Kievan Rus and the Khazars. Both of them converted to Abrahamic Religions, as Abrahamic religions were encroaching closer and closer to their Pagan Empires. The Kievan Rus, converted to Greek Christianity, when Catholicism, Judaism, and Islam were also discussed with him, as it's famously retold, the King of the Kievan Rus, Vladimir the Great, first chose Judaism, but did not accept conversion because the Jews did not have a home or Kingdom of their own, then he chose Islam, but upon hearing the abstention of alcohol, he said, "Drink is the joy of the Russian." and so he chose Greek Christianity, and married and Byzantine Princess, cementing ties with the Roman Empire, and solidifying a Orthodox Christian sphere of influence within the east Slavic people which exists today. The Khazars, were quite similar, it is suggested that they converted to Judaism, as a way to negate the foreign influence of Byzantine Christianity, and Sunni Islam, to provide a formalised faith that was independent from the Patriarch and the Caliph, and showed no factionalist support to the Christian, Tengri and Muslim elements in the Kingdom. But, lets get back to King Hans a year later.
"My King, ever since your... bold proclamation, we have many things to discuss regarding the Kingdom."
"Ah! Steward, due to the changes to our Federal state, I have changed the crown into a small hat with a short, round brim, named after it, I call it the "Fedora."
"Very good, my King, firstly, regarding the treasury. When your highness revoked the privileges of the Church, you gained many riches and lands, however, the Papal Ambassador who left angrily from your court has reported to the Pope, and the Pope has declared you an enemy of God's Church, who has forsaken our saviour-"
"Our 'Saviour', Steward?"
"Apologies my king, 'his saviour' and has pillaged his holy places and oppressed his believers. Our neighbours are encroaching upon our territories, with the intent to conquer us using the declaration of the Pope to back their claims on your ancestral lands."
"Call the banners, Steward! This cannot stand!"
"My Lord, your Marshal has already called the banners to go against the invaders, but unfortunately since the priests left or built their own parishes, they have been obstinate against us, and we no longer have their administration or access to their records of how much wealth or men to call upon. Infact, I have a report from the Marshal, who appears to be having hardship, it seems that some of his soldiers have fled, or turned against him, as the Duke of Milan had his Bishop read out the declaration, that all who serve you will be excommunicated and their souls not be saved."
"Psh, if only they would see reason, send a message to all the Kingdoms who believe that God is Dead, and have them send aid to us."
"Of course your highness, already I have sent riders with fresh horses to every single Kingdom that might assist us in a sense of brotherhood."
*A noise comes from outside the hall, a company of knights and the Kings younger brother, Fredrick burst in!*
"Damned Brother, I have come to take my birthright which you have forsaken and squandered!
"Fred, the hell are you doing here?! You should be fighting the damn Duke of Milan."
"No brother, I have come to take my rightful place, as King of Bavaria! It is my divine right to rule, since you have decided the forsake the Lord!"
"It's not your kingdom, Fred, you didn't inherit it, I did!"
"But it is, Brother, for I, and all good Bavarian Christians, believe in our Saviour, and know that it is God's rightful plan that a true Christian of God's Church rule his people. Now, surrender, by the grace of God, and we shall not harm you."
"Damn you, Fredrick! You cannot stop me, for I am King, and I say so! I will fight you all alone, the only Atheist in all of Allemania!"
*One of the Knights stabs King Hans in the shoulder*
"Ouch! Jesus Christ that hurt!"