I guess the title says it all. However, I have skimmed through several books, and while they all tell you how to use generating functions to find an expression for the n'th term of a recurrence relation, none of them say why it works.
I think I have a somewhat intuitive understanding of what is going on, but I think I need a more definitive explanation.
The generating function method works because it allows you to "handle" the recurrence formula for a sequence $(a_n)$. Indeed if we want to find a closed expression for a sequence $(a_n)$ from a recurrence formula it might be impossible to get the closed formula. Setting :
$$A(X)=\sum_na_nX^n $$
We are able to "translate" the recurrence formula for $(a_n)$ into a nice equation on $A(X)$ (the equation could be polynomial, differential, functional...).
When we do this we strongly believe that we will get an equation, and that this equation will be solvable. Finally we need a good library of generating function to make sure that our solution has explicit coefficients.
To answer your question, using generating function with a sequence $(a_n)$ verifying a recurrence formula is a way to consider the sequence $(a_n)$ as an object and then the recurrence formula is not considered on each $a_n$ anymore but is rather a property that the object $(a_n)$ verifies. Doing this we apply the recurrence formula to each $a_n$ at the same time, there is no doubt that applying the recurrence formula to each $a_n$ we will get more information than applying it to one $a_n$ at the time.
A good reference for this is the book from Herbert S Wilf : $\underline{\text{generatingfunctionology}}$. In it you will see that instead of considering ordinary generating functions :
$$\sum_na_nX^n$$
you could also use exponential generating functions :
$$\sum_n\frac{a_n}{n!}X^n $$
or arithmetic ones :
$$\sum_{n\geq 1}\frac{a_n}{n^s}$$
The generating function you need to use to study $(a_n)$ is strongly related to the recurrence formula it verifies. Hence we understand that the use of generating functions is not magical, when the recurrence formula simply involves lower terms of $a_k$ then we use ordinary generating functions (e.g. Catalan numbers), when it uses lower terms of $a_k$ and $\begin{pmatrix}n\\k\end{pmatrix}$ one should use exponential ones (e.g. Bell numbers) and when it involves a sum over the divisors of $n$ then one should use arithmetic generating functions (e.g. Moebius inversion).