If a (say constant) group $G$ acts on a scheme $X$, you may want to consider the notion of a $G$-sheaf : a sheaf $\mathcal F$ endowed with isomorphisms $\lambda_g: g^* \mathcal F\simeq \mathcal F$, for $g\in G$ satisfying the usual cocycle conditions. Then by functoriality of cohomology for $g:X\to X$ you get an isomorphism $H^i(X, \mathcal F) \to H^i(X, g^*\mathcal F)$ that you can compose with the morphism induced by $\lambda_g$, that is $H^i(X, g^* \mathcal F)\simeq H^i(X,\mathcal F)$. Thus you get for each $g\in G$ an automorphism of $H^i(X, \mathcal F)$ and it is easy to check that this gives an action of $G$ on this cohomology group.
A probably better way to see this is to use functoriality of $G$-sheaves : the global section functor goes from $G$-sheaves of abelian groups to abelian groups endowed with an action of $G$. Since the abelian category of $G$-sheaves has enough injectives (a clessical classical fact, you can find it in Grothendieck's famous Tohoku paper) you can derive it. You get cohomology groups naturally endowed with an action of $G$. Once you apply the forgetful functor, you recover the usual cohomology groups (this is easy to see directly, or you can use Grothendieck's theorem on derivation of a composition of functors, the only point is that the forgetful functor is acyclic).
There is a natural generalization to action of non constant groups, and also to action of monoids.
I think you can apply this in your situation, since the $l$-adic sheaf defining $l$-adic cohomology is naturally endowed with the structure of a $G$-sheaf (the sheaf $\mathbb Z/l^k\mathbb Z$, as any constant sheaf, has a canonical structure of $G$-sheaf).
