When in high school I used to see mathematical objects as ideal objects whose existence is independent of us. But when I learned set theory, I discovered that all mathematical objects I was studying were sets, for example:
$ 0 = \emptyset $
What does it mean to say that the number $ 1 $ is the singleton set of the empty set?
Thank you all for the answers, it is helping me a lot.
Obs.
This question received far more attention than I expected it to do. After reading all the answers and reflecting on it for a while I've come to the following conclusions (and I would appreciate if you could add something to it or correct me): Let's take a familiar example, the ordered pair. We have an intuitive, naive notion of this 'concept' and of its fundamental properties like, for example, it has two components and
$ (x, y) = (a, b) $ iff $ x = a $ and $ y = b $
But mathematicians find it more convenient (and I agree) to define this concept in terms of set theory by saying that $ (x, y) $ is a shortcut for the set { {x}, {x, y} } and then proving the properties of the ordered pair. I.e. showing that this set-theoretical ordered pair has all the properties one expect the 'ideal' ordered pair to have. Secondly, mathematicians don't really care much about these issues.
It means that people have been trying to boil everything down to the least possible amount of data, rules, and symbols. Axiomatisation is a part of this process.
But besides this, unless you really are studying the foundations for some purpose, it shouldn't really bother you or change the way you think of more advanced mathematics. No one is ever going to rewrite functional analysis textbooks from a point of view that acknowledges the fact that at the very beginning, $0$ is $\emptyset$.