[guided]We need to show that every point at which every element of $S$ vanishes also kills every element of the larger set $I_S$. The slogan: passing from a generating set to the ideal it generates does not enlarge the locus of common zeros, because the ideal is built from the generators by exactly the operations (sum and multiplication by ring elements) that preserve the property "vanishes at $p$".
\textbf{Unpacking $I_S$.} The ideal generated by $S$ is, by definition, the smallest ideal of $k[X_0, \ldots, X_n]$ containing $S$. Equivalently, it is the set of all finite $k[X_0, \ldots, X_n]$-linear combinations of elements of $S$:
\begin{align*}
I_S = \left\{ \sum_{j=1}^N g_j\, s_j : N \ge 0,\ s_j \in S,\ g_j \in k[X_0, \ldots, X_n] \right\}.
\end{align*}
This concrete description is what makes the proof go through.
\textbf{Why concrete generators suffice.} Take $[p] \in V(S)$. By hypothesis, $s(p) = 0$ for every $s \in S$. We want to show $f(p) = 0$ for every $f \in I_S$. Pick any $f \in I_S$ and use the description above: write
\begin{align*}
f = \sum_{j=1}^N g_j\, s_j.
\end{align*}
\textbf{Evaluation is a ring homomorphism.} For any point $p$, the map
\begin{align*}
\mathrm{ev}_p : k[X_0, \ldots, X_n] &\to k \\
h &\mapsto h(p)
\end{align*}
is a ring homomorphism: it sends sums to sums and products to products. Therefore evaluating $f$ at $p$:
\begin{align*}
f(p) = \mathrm{ev}_p\left(\sum_{j=1}^N g_j s_j\right) = \sum_{j=1}^N \mathrm{ev}_p(g_j)\cdot \mathrm{ev}_p(s_j) = \sum_{j=1}^N g_j(p)\cdot s_j(p).
\end{align*}
\textbf{Closing the argument.} Each $s_j \in S$, so $s_j(p) = 0$ by hypothesis. Each summand $g_j(p)\cdot s_j(p) = g_j(p) \cdot 0 = 0$, regardless of what $g_j(p)$ is. Hence $f(p) = 0$. As $f \in I_S$ was arbitrary, $[p] \in V(I_S)$.
\textbf{Why ideals (rather than just subsets) are the right invariant for $V$.} What this argument shows is that $V$ "factors through" the ideal-generation operation: only the ideal generated by $S$ matters for $V(S)$. This is the algebraic counterpart of the geometric fact that a closed subvariety is determined by its homogeneous ideal of definition, not by any particular finite generating set.[/guided]