In the notes I am reading, it states: A representation fo an affine group scheme $G$ is a morphism $r: G \rightarrow GL_V$. It is faithful if it is injective.
In this notes they are defining schemes using their functors of points, so here a morphism is a natural transformation, which I understand as equivalent to assigning a map $G(R) \rightarrow GL_V(R)$ for all $k$ algebras $R$ so that given any morphism $R \rightarrow R'$ the diagram (which I don't know how to create on Latex) commutes.
What does it mean for this to be injective? Any explanation would be appreciated. Thank you.
In any category you have a notion of monomorphism, which is often taken as a generalization of the notion of injectivity (in $\mathbf{Set}$ and many usual categories such as $\mathbf{Grp}$, the monomorphisms are precisely the injective maps)
Here "injective" is probably meant as "a monomorphism $G\to GL_V$".
Now I don't know enough algebraic geometry, but there is probably an interpretation of "monomorphism" in terms of the maps $G(R)\to GL_V(R)$, for algebras $R$. For instance if this map is injective for all $R$, then $G\to GL_V$ is a monomorphism; I don't know about the converse, hopefully someone with more algebraic geometry knowledge can fill that gap.
If you look in the category of affine schemes, which is dual to the category of rings, then a map $\hom(A,-)\to \hom(B,-)$ is a monomorphism if and only if the associated $B\to A$ is an epimorphism. But if it is an epimorphism, given $R$, $\hom(A,R)\to \hom(B,R)$ is clearly injective; so in the category of affine schemes, monomorphisms are precisely the maps that are injective on each algebra; however I don't know what happens if you go to schemes.