What does the expression "God takes care of his fools." mean?

I work in an extremely technical environment. One of the guys in the group, an absolutely brilliant microcontroller programmer, is a “believer” (for lack of a better word) and avid Bible reader.
We often encounter strange circuit timing anomalies that he is asked to fix. He methodically goes through the process and eventually finds it. Invariably he uses the aforementioned quote when he describes what he found and the work-around solution.
How should I respond? Right now I just say “Nice work!” or “Good find!”
Meanwhile, I am silently screaming: “Seriously? Do you think God cares that there is a race condition between pin A_Vsr_OTd and pin Clk_240? Really?! And if he cared so much why didn’t he advance said signal by 350 ps to avoid the condition in the first place?!”
But, I just say “Great job!”
What does the expression mean? Is this derived from a Bible quote? Should I just ignore it? Is there a better way to respond?

Note: I am even less religious than a certain raging alien here. However, I want to be respectful and continue to work well with all the staff.