No, $S$ does not have to span $C(X)$.
Taking the case with $X=[0,1]$, let $\mu$ be any atomless finite signed measure whose positive and negative parts $\mu^+$,$\mu^-$ have full support, so that $\mu^+(U) > 0$ and $\mu^-(U) > 0$ for any nonempty open $U$. Then, the set $S=\{f\in C(X)\colon\int f\,d\mu=0\}$ satisfies your properties, is closed in $C(X)$, but is not all of $C(X)$.
To see that $S$ satisfies your properties, consider any $a\in U$ for $U$ an open subset of $X$. Then choose $r > 0$ such that $V=U\setminus \bar B_r(a)$ is nonempty. There exists a nonnegative $g\in C(X)$ with support in $V$ such that $\mu(g) > 0$. Otherwise we would have $\mu^+(S)\le\mu^-(S)$ for all Borel $S\subseteq V$, which would imply that $\mu^+(V)=0$ contradicting the assumption that $\mu^+$ has full support. Similarly, there is a nonnegative $h\in C(X)$ with support in $V$ and $\mu(h) < 0$. By scaling, we can assume that $g,h$ are bounded by $1$.
Now, the functions $f_n(x)=\max(1-n\vert x-a\vert,0)$ have support in $B_r(a)$ (for $n > 1/r$) and decrease to $1_{\{x=a\}}$ as $n\to\infty$. As $\mu$ is atomless, we have $\mu(f_n)\to0$. Choosing $n$ large enough that $\mu(h) < \mu(f_n) < \mu(g)$ then $f=f_n+\lambda h$ or $f=f_n+\lambda g$ will satisfy $\mu(f)=0$ for some $0\le\lambda\le1$. But, $f\in S$ satisfies (i) $0\le f\le1$, (ii) $f(a)=1$, and (iii) $f=0$ outside of $U$.
As such measures $\mu$ will always exist on any compact metric space without isolated points, your conclusion does not hold on any compact metric space other than when $X$ is countable.
If your sequence of functions $r_\alpha$ is uniformly equicontinuous, then this result should hold. That is, there should be one modulus of continuity for all functions in the sequence. Note that the sequence of @i707107 does not satisfy this stronger property. The proof goes along the same lines as the proof that C([0,1]) with supremum norm is a Banach (i.e. complete) space.
Best Answer
Yes, and even more is true. The argument is as follows: let $f\colon X \to \mathbb R$ be a continuous function and let $K\subset X$ be a compact set. Then $f|_K$ is uniformly continuous; let $\omega$ be its nondecreasing subadditive modulus of continuity. By McShane-Whitney's extension formula $f|_K$ admits a uniformly continuous extension to $X$ with the same modulus - more concretely, $$F(x)=\inf\{f(k)+\omega(d(k,x))\colon k\in K\}$$ is this extension which is uniformly continuous on the whole $X$.