Suppose we make a rational argument for some conclusion, C. The argument contains a set of premises, P1, P2, P3...PN.
In any argument relevant to our rational faculties, one might be tempted to claim that, since P1-PN contain no explicit guarantee of rational capacity, one ought not have confidence in the conclusion of the argument, because we cannot trust our faculties to have followed the argument in the first place.
At first, such a critique may seem clever, but it's actually total nonsense.
Implicit in every rational argument is an initial premise, P0, which says that we assume that we are rational and that the problem under study is amenable to rational analysis. That is, P0 assumes axioms of rationality, including logical consistency, induction, and the axiomatic nature of our experiences.
Without this implicit premise, no rational arguments would work.
There's a simple way of stating this result. We cannot have a rational argument for the axioms of rationality. Any such argument would rely on the axioms it was trying to prove.
That means that any supposed rational argument that states that God guarantees our rationality (and a world where such faculties are applicable) is circular. In order to find such a rational argument persuasive, I would first have to assume that I am rational in order to prove that I am rational.
Implicitly, a naturalistic argument about origins incorporates P0. If a theist later says "ah, but your argument must make the additional assumption that the naturalistic process made us rational," then the theist would be slipping on a logical banana skin. The original argument, like all rational arguments, assumed we were rational in step zero, so it costs us nothing to reassert this assumption later.
Likewise, any rational argument we make that refers to God also incorporates P0. That means we are immune from atheists asking questions like "how do you know God isn't just making you think you're rational?"
This doesn't mean we cannot critique a rational argument on the grounds that it contradicts the rational faculties upon which it relies. However, in order to use this approach, we have to show that P1-PN truly contradict P0. We have to show that the premises that follow P0 make rationality totally impossible. Accusing an argument of making rationality improbable is not adequate to invalidate an argument on these grounds.
Christianity falsely pretends that the axioms of reason are rationally deduced from the axioms of Christianity. Christians would have us believe that the assumption of their theology grants us rationality, and creates a lawful universe in which science and rationality are possible. This is hijacking, plain and simple. If we did not assume rationality (which includes inductive inference), then the assumption of God wouldn't guarantee anything at all (not even itself).