Let's look at something you are hopefully more familiar with and that is the complex and real numbers. Every complex number can be written uniquely as $a + bi$ with $a, b \in \mathbf R$. This means that $\{1, i\}$ is linearly independent over $\mathbf R$ (it is a basis of $\mathbf C$ over $\mathbf R$). A linear transformation of $\mathbf C$ over $\mathbf R$ is a function $T : \mathbf C \to \mathbf C$ such that
- $T(w + z) = T(w) + T(z)$ for every $w, z \in \mathbf C$
- $T(az) = aT(z)$ for every $z \in \mathbf C$ and $a \in \mathbf R$
Every such transformation takes the form
$$ T(a + bi) = (ar + bs) + (at + bu)i, $$
for some real numbers $r,s,t,u$. We can write this equation in matrix form as
$$ \begin{pmatrix} r & s \\ t & u \end{pmatrix} \begin{pmatrix} a \\ b \end{pmatrix} = \begin{pmatrix} ar + bs \\ at + bu \end{pmatrix}. $$
For instance, the complex conjugation map $T(a + bi) = a - bi$ corresponds to the matrix equation
$$ \begin{pmatrix} 1 & 0 \\ 0 & - 1 \end{pmatrix}\begin{pmatrix} a \\ b \end{pmatrix} = \begin{pmatrix} a \\ -b \end{pmatrix}. $$
We can also consider the map $T(a + bi) = (c + di)(a + bi)$ (that is, $T$ multiplies on the left by $c + di$). Expanding this out we have
$$T(a + bi) = (c + di)(a + bi) = (ac - bd) + (ad + bc)i, $$
which corresponds to the matrix equation
$$ \begin{pmatrix} c & -d \\ d & c \end{pmatrix} \begin{pmatrix} a \\ b \end{pmatrix} = \begin{pmatrix} ac - bd \\ ad + bc \end{pmatrix}. $$
For ${\rm GF}(2^k)$ over ${\rm GF}(2)$ it is the same idea but instead of $\{1, i\}$ as a basis you have some other basis.