The big difference here is that, given enough time and patience, you will be able to understand every line of code in the Linux kernel. As for the Bible, you are almost guaranteed that this is not true; according to the Bible itself, we mortals are not meant to understand the ways of God, but worship Him unconditionally. Get it?

See also ignorance is bliss.

Disclaimer: Yes, I am an atheist. Or agnostic. Or simply not religious.