Here's an indirect way of tackling the problem:
Let $F \subset L \subset K$ be a tower of algebraic extensions. The set of $F$-isomorphisms of $L$ will simply be the set of $F$-isomorphisms of $K$ restricted to $L$. This is a consequence of the isomorphism extension theorem: each isomorphism of $L$ extends to an isomorphism of $K$. Note further that any isomorphism for $K$ is determined by its action on a set of basis elements, and if $K$ is Galois, then $K$ contains all of the Galois conjugates of all of the basis elements. Thus, when $K$ is Galois, any automorphism of $L$ extends to an automorphism of $K$.
Notice that we have a tower of fields $\mathbb{Q} \subset \mathbb{Q}( \cos(2 \pi/n)) \subset \mathbb{Q}(\zeta_n)$, where $\zeta_n$ is a primitive $n^\text{th}$ root of unity. Since $\mathbb{Q}(\zeta_n)$ is a Galois extension of the rationals (it's the splitting field for the associated cyclotomic polynomial), it suffices to find its automorphisms and restrict down to the field in question. The automorphisms of $\mathbb{Q}(\zeta_n)$ are determined by their action on $\zeta_n$ itself. Where can $\zeta_n$ be sent? The minimal polynomial for $\zeta_n$ is $\displaystyle \Phi_n(x) = \prod_{\gcd(k, n) = 1 \\ \ \ \ 1 \leq k \leq n} \left( x - e^{2i\pi k/n} \right)$, and since the Galois group of an irreducible polynomial acts transitively on its roots, it follows that we can send $\zeta_n \mapsto \zeta_n^k$ for any $1 \leq k \leq n$ such that $\gcd(k,n) = 1$.
Applying Euler's formula gives $\zeta_n = \cos(2\pi/n) + i \sin(2\pi/n)$ and $\zeta_n^k = \cos(2k \pi/n) + i \sin(2k \pi/n)$. Restricting the automorphism determined by $\zeta_n \mapsto \zeta_n^k$ to the field $\mathbb{Q}(\cos(2i\pi/n))$ gives the automorphism determined by $\cos(2i \pi/n) \mapsto \cos(2i \pi k/n)$.