This answer is not the one that I expected but it solves my problem in a non-elegant way.
I will divide this answer in three parts:
Transform the ellipse with center $(x_c, \ y_c)$ and rotated counter clockwise with angle $\varphi$
$$E(x, y) = ax^2+bxy+cy^2 + dx + ey+f = 0 \ \ \ \ \ \ \ \ \ \ \ \ \ (1)$$
into another ellipse
$$F(u , v) = \left(\dfrac{u}{A}\right)^2 + \left(\dfrac{v}{B}\right)^2 - 1 =0 \ \ \ \ \ \ \ \ \ \ \ \ \ (2)$$
With $A > B$
Scale into a new ellipse of major axis equal 1
$$G(a, b) = a^2 + \left(\dfrac{b}{H}\right)^2 - 1 \ \ \ \ \ \ \ \ \ \ \ \ \ (3)$$
Compute the new point $(u_0, \ v_0)$ using the translation and rotations operations of point $(x_0, y_0)$
Compute $(a_0, \ b_0)$ by scaling $(u_0, \ v_0)$
Compute $(a, \ b)$ such we get the minimal distance from $(a_0, \ b_0)$ to $(a, \ b)$
Scale, rotate and translate back
Part 1: Ellipse transformation
We can describe the variable $x$ and $y$ using
$$
x = u \cdot \cos \varphi + v \cdot \sin \varphi + x_c \ \ \ \ \ \ \ \ \ \ \ \ \ (4)
$$
$$
y = -u \cdot \sin \varphi + v \cdot \cos \varphi + y_c \ \ \ \ \ \ \ \ \ \ \ \ \ (5)
$$
With $(1)$, $(2)$, $(4)$ and $(5)$ we can solve it. The computations are a little bit hard but we get
The center
$$
x_c = be-2cd
$$
$$
y_c = bd-2ae
$$
The angle
$$
\varphi = \dfrac{1}{2}\arctan\left(\dfrac{b}{c-a}\right)
$$
The major and minor axis
$$
\kappa = \sqrt{(a-c)^2+b^2}
$$
$$
\eta = \left(f+bde\right) -\left(ae^2+ cd^2\right)
$$
$$
A = \sqrt{\dfrac{-\eta}{a+c-\kappa}}
$$
$$
B = \sqrt{\dfrac{-\eta}{a+c+\kappa}}
$$
Part 2: Scalling ellipse
$$
u = A \cdot a \ \ \ \ \ \ \ \ \ v = A \cdot b \ \ \ \ \ \ \ \ \ H = \dfrac{B}{A}
$$
Part 3: Point transformation
To make a translation we only subtract the center $(x_c, \ y_c)$ and to make a clockwise rotation we put
$$
\begin{bmatrix}
u_0 \\ v_0
\end{bmatrix} = \begin{bmatrix}
\cos \varphi & -\sin \varphi \\
\sin \varphi & \cos \varphi
\end{bmatrix}\begin{bmatrix}
x_0 - x_c \\ y_0 - y_c \end{bmatrix}
$$
Part 4: Scale point
Then we have
$$
a_0 = \dfrac{u_0}{A} \ \ \ \ \ \ \ \ \ \ \ \ \ b_0 = \dfrac{v_0}{A}
$$
Part 5: Compute distance
Let's find the distance of an arbitrary point $(a_0, b_0)$ to the ellipse $(3)$
The distance square is given by
$$
D^2 = (a-a_0)^2 + (b-b_0)^2
$$
Option 3.1: Describe $a$ and $b$ in terms of $\theta$
Let
$$ a = \cos \theta \ \ \ \ \ \ \ \ \ \ \ \ \ \ b = H \cdot \sin \theta $$
Then
$$ D^2 = (\cos \theta - a_0)^2 + (H\sin \theta-b_0)^2 $$
Getting the minimal of $D^2$ we get
$$ \sin \theta (a_0-\cos \theta) - H\cos \theta (b_0-H\sin \theta) = 0 $$
$$ - (1-H^2) \cdot \sin \theta \cos \theta+ a_0 \cdot \sin \theta - Hb_0 \cdot \cos \theta = 0 $$
Then solve for $\theta$ with a numerical method.
Option 3.2: Use Lagrange multiplier
We have the minimizing function $D^2$ with the constraint of $(3)$.
That means we have to find the solution for
$$ \nabla D^2 + \lambda \nabla G = \vec{0} $$ $$ \begin{bmatrix}
2(a-a_0) \\ 2(b-b_0) \end{bmatrix} + \lambda \begin{bmatrix} 2a \\
\dfrac{2b}{H^2} \end{bmatrix} = \begin{bmatrix} 0 \\ 0 \end{bmatrix} $$
Gives us
$$ a = \dfrac{u_0}{1+\lambda} \ \ \ \ \ \ \ \ \ \ \ \ b = \dfrac{v_0}{1+\frac{\lambda}{H^2}} $$
And in $(2)$ gives us
$$ u_0^2 \left(H+\dfrac{\lambda}{H}\right)^2 + v_0^2 \left(1+\lambda\right)^2 - \left(1+\lambda\right)^2
\left(H+\dfrac{\lambda}{H}\right)^2 = 0 $$
Then solve for $\lambda$ with a numerical method
Part 6: Scale back
Once we have $\theta$ or $\lambda$, we can compute the point $a$ and $b$
$$
a = \cos \theta \ \ \ \ \ \ \ \ \ \ \ \ \ \
b = H \sin \theta
$$
or
$$ a = \dfrac{a_0}{1+\lambda} \ \ \ \ \ \ \ \ \ \ \ \ \ \ b = \dfrac{b_0}{1+\dfrac{\lambda}{H^2}}$$
To get the projection point we have to do
$$
\begin{bmatrix}
x \\ y
\end{bmatrix} =
\begin{bmatrix}
\cos \varphi & \sin \varphi \\
-\sin \varphi & \cos \varphi
\end{bmatrix}
\begin{bmatrix}
A \cdot a \\
A \cdot b
\end{bmatrix}+
\begin{bmatrix}
x_c \\
y_c
\end{bmatrix}
$$