In variational calculus, functionals are written as \begin{eqnarray} F = \int f(x,y,y') dx \end{eqnarray}
Where $F$ depends upon choice of $y,y'$. But for smooth regular functions specifying the $y$ also specifies $y'$, so how can they be interpreted as independent?
I also read that functional can be assumed to be function of infinite variables so that derivatives can also be independent infinite variables but this reason seems hard to digest. Can someone please explain me why we don't write just \begin{eqnarray} F = \int f(x,y) dx \end{eqnarray}
and also, why \begin{eqnarray} \frac{\partial}{\partial y}y' &=& 0 \\ \frac{\partial}{\partial y'}y &=& 0 \end{eqnarray}

First of all, $F$ is a functional while $f$ is not. $f$ depends only on finite dimensional vectors. So when you write
$$F[y]=\int_0^1 f(x,y(x),y'(x)) dx$$
you are defining $F$ to be a functional of a rather particular form. For instance it is impossible to choose $f$ such that $F[y]=y(0)$.
Now you are correct that you cannot alter $y'$ without also somehow altering $y$, and can't do very much to $y$ without altering $y'$. However, it is possible to change $y'$ in a "large" fashion while only altering $y$ in a "small" fashion, and functionals of the form above can "detect" when you have done this. (Precisely speaking, the map $y \mapsto y'$ is not bounded.)
For instance, consider the sequence $y_n(x)=\frac{1}{n \pi} \sin(n \pi x)$, $y_0(x)=0$. $y_n$ converges uniformly to $y_0$. Yet $y'_0=0$ while $y'_n=\cos(n \pi x)$: $y'_0$ and $y'_n$ are quite far apart. So the fact that $f$ can depend explicitly on $y'$ means that we can have functionals like
$$F[y]=\int_0^1 y'(x)^2 dx$$
which can see the difference between $y_0$ and $y_n$ for $n>0$ (you will find that $F[y_0]=0$ while $F[y_n]=\frac{1}{2}$ for $n>0$).
More rigorously, if $F$ has the form we started with and $y_n \to y$ uniformly, then we may not have that $F[y_n] \to F[y]$. This would have to happen if $f$ were a continuous function depending only on $x$ and $y(x)$.