Given two vectors, $u$ and $v$, the cross-product with $u$ can be written in matrix form:
$$
\begin{align}
u\times v
&=\begin{bmatrix}0&-u_3&u_2\\u_3&0&-u_1\\-u_2&u_1&0\end{bmatrix}
\begin{bmatrix}v_1\\v_2\\v_3\end{bmatrix}\\[6pt]
&=Y_uv\tag{1}
\end{align}
$$
Suppose $u$ is a unit vector. Then $u\times v$ is the orthogonal projection of $v$ onto the plane perpendicular to $u$ rotated $\pi/2$ (it is perpendicular to both $u$ and $v$).
The orthogonal projection of $v$ onto $u$ is given by
$$
\begin{align}
u(u\cdot v)
&=\left(uu^T\right)v\\
&=Z_uv\tag{2}
\end{align}
$$
The orthogonal projection of $v$ onto the plane perpendicular to $u$ is given by subtracting the orthogonal projection of $v$ onto $u$ from $v$:
$$
\begin{align}
v-u(u\cdot v)
&=\left(I-uu^T\right)v\\
&=X_uv\tag{3}
\end{align}
$$
Thus, rotating $v$ by angle $\theta$ around $u$ would be given by
$$
\left(Z_u+\sin(\theta)Y_u+\cos(\theta)X_u\right)v\tag{4}
$$
Since $X_u+Z_u=I$, the rotation matrix in $(4)$ can be rewritten as
$$
I+\sin(\theta)Y_u-(1-\cos(\theta))X_u\tag{5}
$$
where the matrices $X_u$ and $Y_u$ are given in $(3)$ and $(1)$ above.