I tend to believe that people losing their faiths in religion not because of their misfortunes, but their fortune to be able to live in the modern era, and the availability of alternative explanations. Medieval people suffered a lot more than perhaps any of us, yet they are always feverishly religious, without finding out how much better life could possibly be, or having access to alternatives(they didn't know about Confucianism, and Greek/Latin literatures are off the limit for most people) , you will just choose to believe life is what it should be, because it's the same for everyone, or rather, your material well-being, and everything else is decided by you lineage, you have not seen an exception. Actually, the real revolution of thoughts only happened after the scholars(all of them clerics) started studying works of Antiquity, and learning things that none of them had conceived for the previous hundreds of years. Then slowly it started to transform every aspect of people's life, first the nobles, then the poors.
Also hundreds of years later we are perhaps much more confident with our own judgement, be it about morality or something else, seeing that people here pretty much question God because they are already assertive about certain things being right regardless of God, unimaginable for the Medieval folks.
The main difference between today and Medieval Times is that back then heresy was a crime punishable by torture and death. It is very possible that people back then were tempted to lose their faith even more so than today but were too afraid to speak their minds. If they didn't speak up, you would have no way of knowing about it today would you?
One of the great gifts given to us (in America) by our founding fathers was the freedom of religion and freedom from religious persecution. Now we are free to use our own minds to question our faith and discuss it in, hopefully, rational conversations with others, and through the use of the Internet, all over the world.
Funny you brought up the torture and death, so I figure something should be said about the medieval justice system. For hundreds of years, trial by fire was the prevailing method of determining who is guilty, it stayed in use because, guess what, it somehow worked. People on trial really believed in things like divine intervention, and usually confessed immediately after such a decision was made by the judge.
Now back to the question of whether there were people who are atheistic but were too afraid to speak up, it maybe true there are people who did not speak up due to the fear of torture and death, but I think it's also important to understand why people gradually started to speak up after a certain time point, the fact that theologists like Aquinas would feel the need to reconciliate Christian belief with Greek philosophy and logic, is quite telling.
About the freedom of/from religion, it's true that the American founding fathers were the first with the important foresight to establish it formally as one of the basic principle of the government, probably due to their ancestors' experience of being persecuted religiously, yet it still should be pointed out U.S was not the first nation to treat all religions equally before the law.