In coordinates $(x^0,x^1,x^2,x^3) \equiv (ct, \vec r)$, the index notation simply means that e.g.
$$F^{01} = \partial^0 A^1 - \partial^1 A^0$$
where $(A^0,A^1,A^2,A^3) \equiv (c\phi, \vec A)$ is the 4-potential. In Cartesian coordinates, the Minkowski metric takes the form
$$\eta = \pmatrix{-1 & 0 &0 &0 \\ 0 & 1 & 0 & 0 \\ 0 &0 & 1 & 0 \\ 0 & 0 & 0 &1}$$
and so $\partial^0 = -\partial_0\equiv -\frac{\partial}{\partial (ct)}$ whereas $\partial^i = \partial_i \equiv \frac{\partial}{\partial r^i}$ for $i=1,2,3$. As a result, for $i=1,2,3$ we have
$$F^{0i} = \partial^0 A^i - \partial^i A^0 = -\frac{1}{c} \frac{\partial A^i}{\partial t} - \frac{1}{c}\frac{\partial \phi}{\partial r^i}$$
Recalling that $\vec E = -\frac{\partial \vec A}{\partial t} - \nabla \phi$, the components $F^{0i}$ are simply $E^i/c$. Filling in the rest of the tensor,
$$F = \pmatrix{0& E^1/c & E^2/c & E^3/c \\ -E^1/c & 0 & B^3 & -B^2 \\ -E^2/c & -B^3 & 0 & B^1 \\ -E^3/c & B^2 & -B^1 & 0 }$$
where $\vec B = \nabla \times \vec A$.
So that's how the indicies are defined and how $F$ can be interpreted. Why we would define $F$ in the first place is a deeper and more interesting question.
In the context of special relativity, the fundamental object is $F$, not $\vec E$ or $\vec B$. Given a particular choice of reference frame, we can define 3-vectors $\vec E$ and $\vec B$ by picking out the components of $F$ as shown above, but those components generally mix together when we boost to a different reference frame. In that sense, the splitting of the electromagnetic field into an electric part $\vec E$ and a magnetic part $\vec B$ is artificial and unnatural (though it is of course often useful).
Historically, $\vec E$ and $\vec B$ were understood as distinct objects, not as different aspects of the same thing (i.e. $F$). The Maxwell equations show that despite appearing to be independent, $\vec E$ and $\vec B$ are related to one another very intimately. If you work with the Maxwell equations for a bit, you discover that observers who are in relative motion to one another must observe different electric and magnetic fields - for example, an observer standing next to a stationary charge sees a pure electric field, while an observer moving with respect to the charge sees both electric and magnetic fields.
This naively suggests that the Maxwell equations only work for certain special observers, and that you need to be in the right reference frame to compute the correct fields. However, through an apparent coincidence, it turns out that even though $\vec E$ and $\vec B$ must be different in different frames, they conspire together such that you get the correct trajectory for a particle no matter what frame you work in. The realization that this isn't a coincidence - and that $\vec E$ and $\vec B$ are distinct aspects of a single, fundamental entity - is (at least in part) what fueled Einstein's development of special relativity.
Things get even deeper and more interesting when we move to relativistic quantum mechanics, where electromagnetism arises essentially automatically by imposing something called $\mathrm U(1)$ gauge invariance on the quantum fields. This is far beyond the scope of this question from a technical standpoint, but it is worth mentioning that in this much more advanced (but physically fundamental) context, it is once again $A$ and $F$ which play a fundamental role.