If I have some uncountable proper subset $T$ of transcendental numbers on the real line, by definition I can't count them. Now suppose I take the complement of this set. I now have a set of line segments defined in-between each pair of points, one fewer segments than there were transcendental numbers the original set. But every line segment contains a rational number and therefore the number of segments is countable.
This appears to contradict the independence of the continuum hypothesis from some reasonable maths theory in which the above description is expressed.
Where am I going wrong?
Update: Is the problem that I am defining line segments between distinct rational numbers with potentially no lower limit on length?
Your argument does prove something. Namely, it proves:
(Note that you talk about transcendentals specifically, but there is nothing special about them - we can just talk about reals. And the same statement is true for left-discrete sets, of course.)
The proof is exactly the argument they give. Suppose $X$ were a discrete uncountable set of reals. Then to each $x\in X$ we can assign an interval $I_x$ to $x$: let $I_x=(x, y)$ where $y$ is the next element of $X$.
Now this construction begs the question: $$\mbox{How do we know there is such a $y$ in the first place?}$$ Well, we know that because $X$ is discrete (by assumption). So we're good to go. But note that this step is not true for general $X$.
OK, now we argue as follows. Let $q_x$ be some rational in $I_x$; there are lots of rationals in $I_x$ since $x<y$, so this is doable (and the rationals are well-orderable (not well-ordered - careful!), so we may always "pick one" even without the axiom of choice). But it's easy to show that $I_u\cap I_v=\emptyset$ if $u, v$ are distinct elements of $X$, so the map $x\mapsto q_x$ is an injection from $X$ into $\mathbb{Q}$; and this contradicts the assumption that $X$ was uncountable. $\quad \Box$
(Aw heck, I committed the "logician's sin" - I wrote a proof by contradiction where none is needed! We can just argue directly that if $X$ is right-discrete, then $X$ is countable, by building the injection into $\mathbb{Q}$. I wrote this as a proof by contradiction instead, to better parallel the OP's argument.)
But this is not what you claimed! The result you want is (somehow) that there is no uncountable set of transcendentals; and neither that nor any related statement is true. The only way your argument works at all is if the set in question is assumed to be discrete, or "pretty discrete" anyways.