To get a geometric intuition of matrix transposition, I build upon my geometric intuition of the dot product.
The dot product seen as a projection
One geometric intuition behind the dot product $a \cdot b$ of two vectors is to see it as follow : you first project the first vector $a$ on the second vector $b$, and then you multiply the norm of this projection by the length of the vector $b$.

But since the dot product is commutative, that is $a \cdot b = b \cdot a$, you can also see it as the multiplication of the length of $a$ with the length of the projection of the second vector $b$ on the first vector $a$ (you just need to mentally exchange $a$ and $b$ in the previous drawing).
So when you think of the dot product as a projection, there are $2$ ways to do it : either you project the first vector on the second, or you project the second vector on the first.
Link between transposition and dot product
Let $M$ be some $m$ by $n$ matrix, $a$ a vector of length $n$ and $b$ a vector of length $m$. Let's try to find a matrix a $n$ by $m$ matrix $X$ such that:
$$Ma \cdot b = X b \cdot a $$
There is only one solution to this equation, which is $X = M^T$. Let's interpret this geometrically.
The left part of this equality can be geometrically interpreted as follow :
- Apply the linear transformation $M$ to the vector $a$
- Project the result of this transformation on the vector $b$
- Multiply the length of this projection by the length of $b$
The right part does the exact same thing, but by projecting $b$ on $a$ :
- Apply some linear transformation $X$ to the vector $b$
- Project the result of this transformation on the vector $a$
- Multiply the length of this projection by the length of $a$
And this is where a geometric intuition comes in : if I have some transformation $M$ and I want to intuitively guess what will be its transposition, here are the steps I follow :
- I picture two vectors $a$ and $b$, just as in the above drawing
- I apply mentally apply $M$ that transformation to the vector $a$ and see how the projection (the "shadow") of the vector $a$ behaves.
- I fix the vector $a$ and now I try to move the vector $b$ in such a way that the length of the projection of $b$ on the vector $a$ behaves the same way as the projection of $a$ on $b$.
- If I can find such a transformation of $b$ that matches these requirements, it must be $M^T$ !
Let's apply this with rotations !
Time for intuition training ! Let's intuitively guess what the transposition of a rotation should be by following the previous steps :
- Picture two vectors $a$ and $b$ like the picture above
- Rotate the vector $a$ by some angle $\phi$ smaller than $\theta$ towards the vector $b$. The length of the projection increases.
- Now instead of rotating $a$, rotate the vector $b$ by the same angle $\phi$. This should rotate $b$ away from the vector $a$. Also the length of the projection of $b$ on $a$ decreases. So this is not what we want ...
- Let's try to rotate $b$ in the other direction, that is towards the vector $a$. Now the projection increases. It looks like the rotation $-\phi$ should give us what we want.
And this is indeed the case !
Now you can try that thought experiment for other kinds of transformations. It's not always easy, but it's rewarding, because the transposition is way more than just a diagonal symmetry on a grid of numbers !