Let's say we have a root $b$ of $\Phi_r$. We wonder what the degree of the minimal polynomial of $b$ in $\Bbb{F}_p$ so we can find a factor of $\Phi_r$. We can do this using Galois theory by finding the number of automorphisms of $\Bbb{F}_p(b)$ that fix $\Bbb{F}_p$.
It is well known that all automorphisms of $\Bbb{F}_p$ must be in the form of $\sigma(x)=x^{p^n}$ for some integer $n$. If we have a primitive $r$-root of unity $b$, then for any integer $n$, $b^{p^n}$ must also be a primitive $r$-root of unity because $p^n$ is coprime with $r$. Thus, all of the automorphisms $\sigma(x)=x^{p^n}$ are valid because they all map $b$ to another root of $\Phi_r$. However, once we get to $\sigma(x)=x^{p^a}$, since $p^a \equiv 1 \pmod 4$, this is just the identity automorphism again, so we are repeating ourselves after $a$ automorphisms. Thus, there are $a$ automorphisms in the Galois group of $\Bbb{F}_p(b)$ over $\Bbb{F}_p$.
This means for all of the roots of $\Phi_r$, their minimal polynomial has degree $a$. All of these minimal polynomials must divide $\Phi_r$ because otherwise, there would be no way $\Phi_r$ would have them as roots. Therefore, since all of the irreducible polynomials dividing $\Phi_r$ have degree $a$ and $\Phi_r$ has degree $\phi(r)$, $\Phi_r$ is a product of $\phi(r)/a$ irreducible factors with degree $a$.