I am having some confusion concerning the Frobenius morphism of an elliptic curve over a finite field $\mathbb{F}_q$ with $q = p^r$ and $p$ prime.
I am working with Silverman's "Arithmetic of Elliptic Curves" and currently on the following example:

My question is, if the Frobenius endomorphism fixes exactly $E(\mathbb{F}_q)$ and further $E^{(q)}=E$, what does this endomorphism do? Isn't it then just the identitly, leaving every point fixed? Or shouldn't it fix the points $E(\mathbb{F}_p)$? I just don't see what the frobenius morphism does on an elliptic curve over a finite field, if all the points in questions are left fixed.
I hope someone understands my, a little messy and unclear, question and can help me to free the knot in my head.
The Frobenius $\phi_q$ fixes $E({\Bbb F}_q)$ as shown but doesn't fix the points in $E({\Bbb F})$ where ${\Bbb F}_q\subset{\Bbb F}$ is a field extension.
As an analogy, you should think of an elliptic curve defined over the real field $\Bbb R$ (Weierstrass equation with real coefficients). Then the complex conjugation fixes the real points $E({\Bbb R})$ but acts as a non-trivial involution on the set of complex points $E({\Bbb C})$.