D3 was never intuitive for me. Maybe the problem is that it tries to do too much, at too many different level of abstraction? If it's just about projecting data, that's easy enough to understand. But I guess projection is also closely tied to axis and other pieces.
I found resources like Scott Murray's "Interactive Data Visualization for the Web" to be invaluable; the D3 docs are too dense/reference-focused for me, but his book introduced the concepts in a slower, more tutorial-like fashion.
D3 was never intuitive for me. Maybe the problem is that it tries to do too much, at too many different level of abstraction? If it's just about projecting data, that's easy enough to understand. But I guess projection is also closely tied to axis and other pieces.