Proved this in the end by piecing together bits of information from answers, comments and links provided in this post. Let me know of any places where there are mistakes. These are the steps of the proof I put together:
As in the original post, continue using the notation $F:= \mathbb{Q} (\omega_n)$ and $\Gamma$ for the set of automorphisms of $F$.
Assume $n \geq 3$ because the main theorem that we want to prove is trivial for $n=1$ and $n=2$. Then $\omega _{n} \notin \mathbb{Q}$.
The following two results are some that I have read a proof of in the past. Probably should have put it in the "results I know" section of the original post, but did not know they would be used.
(1) State result on constructing field using irreducible polynomial of $K[x]$ where $K$ is a field
Let $K$ be a field. Let $p(x) \in K[x]$ be a polynomial of degree $d$ that is irreducible over $K$. Let $\langle p(x) \rangle$ be the ideal generated by $p(x)$. Then $K[x] / \langle p(x) \rangle$ is a field. Furthermore, if $\alpha = x + \langle p(x) \rangle $ then every element of $K[x] / \langle p(x) \rangle$ can be expressed uniquely in the form $ k_{d-1} \alpha ^{d-1} + \dots + k_{1} \alpha ^{1} + k_{0} $, where $k_{i} \in K$ for each $i \in \{ 0,1, \dots ,d-1 \}$.
(2) State result on isomorphism between an algebraic field extension of $K$ and a quotient of $K [x]$
Suppose $K$ is a subfield of $\mathbb{C}$. Let $p(x) \in K [x]$ be an irreducible polynomial. Let $\rho \in \mathbb{C}$ be a root of $p$. Then there exists a field isomorphism $\psi : K ( \rho ) \rightarrow K [x] / \langle p(x) \rangle $ with $ \psi ( \rho ) = x + \langle p(x) \rangle $.
(Could generalise this to fields other than $\mathbb{C}$ but this result is enough for what we need.)
(3) Show $\{ 1, \omega_{n} , \dots , \omega ^{d-1} \}$ is basis for $\mathbb{Q} (\omega _{n} )$, where $d$ degree of minimal polynomial of $\omega _{n}$ over $\mathbb{Q}$
Let $m(x) \in \mathbb{Q}$ be minimal polynomial of $\omega _{n}$ over $\mathbb{Q}$. By (2), there exists an isomorphism $ \psi_{1} : \mathbb{Q} ( \omega _{n} ) \rightarrow \mathbb{Q} [x] / \langle m(x) \rangle $ with $ \psi_{1} ( \omega _{n} ) = x + \langle m(x) \rangle $.
Using (1) and the isomorphism $ \psi_{1}^{-1} $, we can see that $\{ 1, \omega_{n} , \dots , \omega ^{d-1} \}$ is basis for $\mathbb{Q} (\omega _{n} )$, where $d$ degree of minimal polynomial of $\omega _{n}$ over $\mathbb{Q}$.
(4) Find all of the roots of $m(x)$ and show degree of $m(x)$ is $ \phi (n) $
Using proof from this post,
prove cyclotomic polynomial is a minimal polynomial
we know that the minimal polynomial is
\[
m(x) = \prod _{\substack{ k \in \{ 1, \dots , n\}, \\ gcd(k,n) = 1 } } (x- \omega _{n}^{k} ) .
\]
We can see this has $ \phi (n) $ distinct roots, where $ \phi(n) $ is the number of positive numbers less than $n$ that are coprime to $n$. Can also see $m(x)$ has no repeated roots. So $ \phi (n) $ is the degree of $m(x)$. Another fact we can see is each root generates the group $ \langle \omega _{n} \rangle $.
(5) Prove $\Gamma$ acts transitively on roots of $m(x)$
Let $ \psi _{1} $ be the isomorphism defined in (3). Let $ \omega_{n} ^{\prime} $ be a root of the minimal polynomial $m(x)$. Then by (2), there exists an isomorphism $ \psi_{2} : \mathbb{Q} ( \omega _{n}^{\prime} ) \rightarrow \mathbb{Q} [x] / \langle m(x) \rangle $ with $ \psi_{2} ( \omega _{n}^{\prime} ) = x + \langle m(x) \rangle $.
Now $ \mathbb{Q} ( \omega _{n} ) = \mathbb{Q} ( \omega _{n}^{\prime} ) $ because we saw in (4) that $ \langle \omega _{n} \rangle = \langle \omega _{n}^{\prime } \rangle $. It follows that $ \psi_{1} \circ \psi_{2} \in \Gamma $ with $ \psi _{1} ( \psi _{2} ( \omega _{n} ) ) = \omega _{n} ^{\prime }$. Clearly this means that $ \Gamma $ acts transitively on the roots of $m(x)$.
(6) Show the set of elements fixed by all automorphisms is a subfield of $\mathbb{Q} (\omega_n)$ containing $\mathbb{Q}$
Let $A = \{ \alpha \in F: \sigma (\alpha ) = \alpha \text{ for all } \sigma \in \Gamma \}$. Let $ \alpha, \beta \in A $. Then,
\[
1 = \sigma (\alpha \alpha^{-1} ) = \sigma (\alpha ) \sigma (\alpha^{-1} ) = \alpha \sigma (\alpha^{-1} ).
\]
Hence $ \sigma (\alpha^{-1} ) = \alpha^{-1} $. Similarly $\sigma (- \alpha ) = - \alpha$. So $ \sigma (\beta \alpha^{-1} ) = \beta \alpha^{-1} $ and $ \sigma (\beta - \alpha ) = \beta - \alpha $.
This shows $A$ is a subfield of $F$. Clearly $\mathbb{Q} \subseteq A$ by the definition of $\Gamma$.
(7) Find minimal polynomial of $ \omega _n $ over $A$
Let $m^{*} (x) \in A[x]$ be the minimal polynomial of $ \omega _n $ over $A$. Since $\mathbb{Q} \subseteq A$ and $ \omega _n$ is a root of the minimal polynomial $m(x) \in \mathbb{Q}$, it follows $m^{*} (x)$ divides $m(x) $.
Let $ \omega_{n} ^{\prime} $ be a root of $m(x) $ then $\sigma ( \omega _n ) = \omega_{n} ^{\prime} $ for some $ \sigma \in \Gamma$.
By the definition of $A$, the coefficients of $m^{*} (x) $ are fixed by $\sigma$, so $0 = \sigma (0) = \sigma (m^{*} (\omega _n) ) = m^{*} ( \sigma (\omega _n) ) = m^{*} ( \sigma ( \omega_{n} ^{\prime} ) $. Hence $\omega_{n} ^{\prime} $ is a root of $m^{*}$. So $ m(x) $ divides $ m^{*} (x) $. Hence $ m(x) = m^{*} (x) $.
(8) Prove the main result
Notice $ A( \omega _{n} ) = \mathbb{Q} ( \omega _{n} ) $ because $A \subseteq \mathbb{Q} ( \omega _{n} ) $ and $ \mathbb{Q} \subseteq A$. Using (1) and (2), every element of $ \mathbb{Q} ( \omega _{n} ) $ can be expressed uniquely as in the form $ a_{d-1} \omega _{n} ^{d-1} + \dots + a_{1} \omega _{n} ^{1} + a_{0} $, where $d $ is the degree of $m(x)$ and $a_{i} \in A$ for each $i \in \{ 0,1, \dots ,d-1 \}$.
Suppose $A \neq \mathbb{Q}$. By definition, $ \mathbb{Q} \subseteq A$, so there exists $ a \in A \setminus \mathbb{Q}$. Then $a = a \cdot 1$ when expressing $a$ as an element of $\mathbb{Q} ( \omega _{n} ) $ as an $A$-vector space.
But when expressed as an element of $\mathbb{Q} ( \omega _{n} ) $ as an $\mathbb{Q}$-vector space, $a = q_{d-1} \omega _{n} ^{d-1} + \dots + q_{1} \omega _{n} ^{1} + q_{0} $ where $q_{j} \in \mathbb{Q}$ for each $j \in \{0,1, \dots , d-1 \}$ and most importantly $q_{k} \neq 0$ for some $k \neq 0$.
But $ q_{d-1} \omega _{n} ^{d-1} + \dots + q_{1} \omega _{n} ^{1} + q_{0} $ is also a linear combination of basis elements with coefficients in $A$. So we have two distinct linear expressions for $a$ when looking at $\mathbb{Q} ( \omega _{n} ) $ as an $A$-vector space.
This is a contradiction. Thus $A = \mathbb{Q}$.