Here's a direct proof, arguing by induction on $n$, and then on the common order $k\ge 1$ of the that if permutation matrices $A,B$, that if $A,B$(of size $n\ge 0$) have the same characteristic polynomial (or equivalently are linearly equivalent, since these are diagonalizable) then they are conjugate as permutations, i. For $k=1$ we have $A=B=I_n$e. Assume $k\ge 2$, have the same cycle decomposition.
If $A,B$ have some cycle of common size, then we can "remove" it (which divides the characteristic polynomial by the same factor while reducing the matrix size). So we can suppose there are no cycles of common size. Let $p$ be a prime divisor of $k$. Thenlength in $A^p$$A$ and $B^p$ are linearly conjugate$B$. In this case, and hence by inductionwe have the same cycle decomposition. Each cycle of order $pq$ (for some $q\ge 1$) for $A^p$ orto prove that $B^p$ comes from$n=0$.
Consider a cycle of ordermaximal length $p^2q$$m$ occurring in botheither $A$ andor $B$. Hence there is none. Thus, $k$ is a square-free number, say $k=p_1\dots p_\ell$ (we suppose by contradiction $k\ge 2$, that is,in $\ell\ge 1$)$A$. The existence of a $k$-cycle means that the root of unityThen $\exp(2i\pi/k)$$\xi=\exp(2i\pi/m)$ is a root of the characteristic polynomial which is a property shared byof $A$, and $B$; hence $A$ and $B$ have no $k$-cycle. Consider a cycle of maximal length $r$ occurring in $A$ or $B$, say in $A$; we can suppose that $p$ does not divide $r$. ThenBut since $A^p$$B$ has the same cycleonly cycles of length $r$. But it is permutation conjugate to $B^r$, which has no such large cycle$<m$, sinceits characteristic polynomial does not vanish at $B$ has none. We$\xi$, and we get a contradiction.