I'm sorry, but a program that's thousands of methods and small classes is not clearer than a program with fewer, larger, structures. Yes, write code for Humans, not machines, I agree. BUT remember your other programmers want to understand your program - not any one individual method - so making each method simple only moves the complexity into the interrelationships between methods, something considerably harder to understand.
What the author was implying is that you should take relatively straightforward components of a function and break them out as their own sub-functions with a very descriptive name, especially the inner workings of nested loops. If you take the inner loop and replace it with a function call that describes what the inner loop does, then your outer loop actually gets much easier to read, as it does not have the distraction of the gritty details of how the inner loop performs its duties. With properly written sub-functions, you can simply read the name and understand what it is doing without having to actually read the function at all. I have personally done code reviews on code that has been re-factored in this fashion, and the readability of the code is night and day.