From what I understand, your question comes down to why a set being ordered does not imply it being countable.
The slightly subtle notion here is the difference between cardinal and ordinal numbers. In general, there are two standard ways to compare the sizes of two sets. You can construct a bijection (as you've probably seen), or you can construct an order-preserving bijection.
For instance, you've probably seen a bijection between $\mathbb{N}$ and $\mathbb{Q}$, but there is no order preserving bijection, so we say both sets have cardinal number $\aleph_0$ but ordinal numbers $\omega$ and $\omega^2$ respectively.
More visual perhaps is the difference between $A=\{1,2,3,...\}$ and $B=\{1,3,...,2,4,...\}$. In one case all the natural numbers are listed sequentially. In the second, all odd numbers come before the first even. We have clearly that $|A|_{card}=|B|_{card}$, but we say that $|B|_{ord}=\omega * 2$.
Now, the notion you want here is well ordering. A set is well ordered if every subset has a least element. In that sense, if we use an assumption called the axiom of choice, we can construct a well-ordered set which is uncountable, but we will never be able to completely describe it (and that's one reason why the axiom of choice has been somewhat controversial).
Given these assumptions, a well ordering of a uncountable set will contain lots and lots of ...'s. So for instance, we can write the open interval $(0,1)=\{0.1, 0.11, 0.111,...0.2, 0.22, 0.222, ..., 0.21, 0.211,...\}$, but its clear we will never be able to list all the terms in that set in a way we can assign a natural number to every term. Nonetheless, it can be shown that there existis some well ordering of every uncountable set, but this ordering will certainly not be the same as the regular ordering of $\mathbb{R}$