I can understand how the Greek alphabet came to be prominent in mathematics as the Greeks had a huge influence in the math of today. Certain letters came to have certain implications about their meaning (i.e. $\theta$ is almost always an angle, never a function).
But why did $x$ and $y$ come to prominence? They seem like $2$ arbitrary letters for input and output, and I can't think why we began to use them instead of $a$ and $b$. Why did they become the de facto standard for Cartesian coordinates?

Classically "x" was always used in the sciences for denoting an unknown quantity, e.g. the "X-rays" of Röntgen.
Cajori has a nice discussion in "A History of Mathematical Notations". In brief, Descartes's convention was to use letters from the earlier half (a,b,c...) for known quantities and from the latter half (x,y,z...) for unknowns. This was in the 1600s if I remember correctly.