Not every subset of $\mathbb{R}$ is Borel. Wikipedia gives an example of a non-Borel set, citing Kechris, Descriptive Set Theory; the construction is sufficiently complicated that I too will defer to Kechris here.
Now, you might say: given a set $A$, can't we just write $$A=\bigcup_{a\in A}{\{a\}}$$ and conclude that, since each $\{a\}$ is Borel, so is $A$? No, because the union defining $A$ need not be countable. There is a term in the union for each element of $A$, and $A$ can be quite large indeed. In the example Wikipedia cites, $A$ is equinumerous with $\mathbb{R}$.
Now, you might say: OK, but can't we write down some sort of list of Borel sets, rather than starting with the open sets and then taking closure under some operations? Actually, one can. But it's not as interesting as you might hope.
The key is to recognize that the axioms of a $\sigma$-algebra in fact encode logical formulas. The atomic formulas are any proposition of the form "$x\leq c$" for some constant $c$. "And" and "or" correspond to intersection and union; negation to set complements, and we can quantify over $\mathbb{Q}$ since the universal quantifier is a countable intersection. To be precise, let $\mathscr{L}=\{\leq\}\sqcup\{r:r\in\mathbb{R}\}$ be the language with one relation and $|\mathbb{R}|$-many constant symbols. Thus $S$ is Borel iff $S=\{x:\phi(x)^{\mathbb{R}}\}$, where $\phi$ is an infinitary ($\mathcal{L}_{\omega_1,\omega}$) logical formula in $\mathscr{L}$ that quantifies only over $\mathbb{Q}$, and where the superscript is to indicate that the symbols in $\mathscr{L}$ are interpreted in the obvious way. (In fact, since the continuous preimage of an open set is open, you can use continuous functions in $\phi$ too.)
That logical representation also underlies the counting argument Noah Schweber mentioned. There are only $|\mathbb{R}|\times|\mathbb{N}|=|\mathbb{R}|$-many such formulas, so there are only as many Borel sets as there are real numbers. But there are definitely more subsets of $\mathbb{R}$ than that.
(I screwed up describing the logic for formulas characterizing Borel sets; h/t Noah Schweber for the correct name.)