Note: This is an extension of my comment above. As I said there, I'm not very used to the definiton of manifolds as functionally structured spaces, but I think that the following works. The idea comes from the similar question found here. Any comments on possible mistakes are welcome.
Answer: According to Bredon's definition 2.4, a diffeomorphism is defined as an isomorphism of structures, hence it suffices to show (according to definition 2.3) that there are open sets $U \subseteq X$ and $V \subseteq \mathbb{R}$ such that no isomorphism between $(U, F_X(U))$ and $(V, C^\infty(V))$ exists.
Assume there exists such an isomorphism $\varphi: X \rightarrow \mathbb{R}$, and let $U \subseteq X$ and $V \subseteq \mathbb{R}$ be two neighborhoods around the origin (for example $U = X$ and $V = \mathbb{R}$). Then the induced maps on the structures are given as
\begin{equation}
\phi: C^\infty(V) \rightarrow F_X(\varphi^{-1}(V)),\quad f \mapsto f \circ \varphi
\end{equation}
and
\begin{equation}
\tilde \phi: F_X(U) \rightarrow C^\infty(\varphi(U)),\quad f \mapsto f \circ \varphi^{-1}
\end{equation}
Now consider the map $\pi_2(x,y) = y$, i.e. the projection onto the second coordinate in $\mathbb{R}^2$. This is a smooth map around the origin in the plane, hence $f := \pi_2\mid_U \in F_X(U)$. Now, since $\varphi$ is an isomorphism, we need to have a counterpart of $f$ in $C^\infty(\varphi(U))$. But the map
\begin{equation}
\tilde\phi(f) = \pi_2\mid_U \circ \varphi^{-1}
\end{equation}
is not smooth around the origin, hence $\tilde\phi(f) \notin C^\infty(\varphi(U))$, a contradiciton. So there exists no isomorphism of structures between $(X, F_X)$ and $(\mathbb{R}, C^\infty)$, what means that they are not diffeomorphic to each other.