I just glanced at Yvain's spreadsheet and it looks like 681 people gave probabilities less than 1% (AKA .01 as per survey formatting) and many of those entered simply 0 which couldn't be misinterpreted either way. With about a thousand responses, <1% is the most prominent response given. No idea what data the OP could be looking at.
The 2012 LessWrong Censur had a question about belief in God. It also had a question about how people self label their religious beliefs. Interestingly 6.69% of the nonspiratual atheists believe that it's more likely that a God exists than that no God exists. On the other side of the spectrum 17% of the committed theists believe that the chance that God exists is only 2%. Those 2% are the median for nonspirtual atheists who belief in God.
Not a single person who took the LessWrong census believes that the chance that God exists is less than 1%. Given that this community has quite a lot of contrians and quite a lot of skeptics I would have guessed that there are people who believe that the chance that a God exists is less.
The orginal question on the survey was:
The numbers make also a nice plot:
There's also the question:
Given those results what do you think if someone tells you that they are atheist or a theist?