Basically it's more fundamental because if you try to bootstrap mathematics from set theory you need a set of 10 axioms which seem unmotivated and disconnected. To bootstrap math from category theory invokes stepping through a rich series of theories starting from the merest notion of "combining things" and moving upward. It helps us see the foundations of mathematics as living within a large universe of alternative, slightly differing foundations and therefore recognize the somewhat "arbitrary" nature of standard math foundations. In many ways this is a more appealing sort of foundations. Category theory requires sets to "bootstrap" itself, but you can get by with a naive construction and work up from there.