Note: Better answer below, leaving for posterity. Let's assume for now that $\Omega=\mathbb{R}$ and $\mathcal{F}$ is the Borel $\sigma$-algebra, and let $\mu$ be the given measure on $\mathbb{R}$. Then we can write $\mu((-\infty,x])=g(x)$ for some monotonic $g$, and as we have no atoms $g$ is continuous. Let $X^{-1}((-\infty,x])=(-\infty,f(x)]$ for some monotonic increasing $f(x)$ satisfying $f(\mathbb{R})=\mathbb{R}$, i.e. $\{X(\omega)\leq x\}\Leftrightarrow\{\omega\in(-\infty,f(x)]\}$. This is equivalent to defining $X(\omega)=y$ for all $\omega\in[\lim_{z\uparrow y}f(z),f(y)]$, which is well-defined if $f(\mathbb{R})=\mathbb{R}$. Then we can show that $\mathbb{P}[X\leq x]=g(f(x))$. So now the questions becomes, can we make $g(f(x))$ differentiable on all of $\mathbb{R}$ for arbitrarily weird functions $g$ that are continuous and satisfy $g(-\infty)=0$, $g(\infty)=1$?
I believe the answer is yes, and I've heard claims to that effect, but I can't find an actual proof. It's more of an analysis question, and an elementary enough one, so if you post a question with the analysis tag one of those guys might be able to help you out.
Update: Thanks to @Did for the clarification. It's sufficient to be able to construct a random variable uniformly distributed on the set $\{\frac{i}{2^n}\}_{i=1}^{2^n}$ for any $n$. Use the axiom of choice to inductively create the following partitions. For $n=1$, let $E_1^{(1)}$, $E_2^{(1)}$ partition $\Omega$ and satisfy $\mathbb{P}[E_i^{(1)}]=\frac{1}{2}$ for $i=1,2$. For general $n\geq 2$ and $1\leq k\leq 2^{n-1}$, let $E_{2k-1}^{(n)},E_{2k}^{(n)}$ partition $E_k^{(n-1)}$ into two sets of equal probability. Let $X_n(\omega)=\frac{1}{2^n}\sum_{i=1}^{2^n}i1_{\omega\in E_i^{(n)}}$. Then $X_n$ is uniformly distributed on the set $\{\frac{i}{2^n}\}_{i=1}^{2^n}$. Furthermore for every $\omega\in\Omega$ $X_n(\omega)$ is monotonically decreasing as $n\rightarrow\infty$, so $X_n$ converges pointwise (and therefore almost surely) to some random variable $X$. But almost sure convergence implies convergence in distribution so $X$ must be a $\text{Uniform}[0,1]$ random variable.