What must be trusted in Coq in the kernel, which contains 30,000 lines of code for the latest development version.
It cannot be completely verified by Coq itself due to the Gödel theorem (well, now with this bug this is possible). Still, some part of it can be verified, like the byte-code interpreter. There is actually an ongoing project to make a certified JIT compiler for Coq: http://www.maximedenes.fr/download/coqonut.pdf
Doesn't the Gödel theorem say that such proof cannot be found for all conceivable systems; but that for any particular system, a proof could in principle be found?
I think it's something like this: you can't prove the consistency of a formal system using that same formal system, unless it is in fact inconsistent, but you can model a formal system from inside a larger formal system and then prove things like consistency about the smaller system from inside the larger one. But then the consistency of the larger system is unproven and you're stuck with an endless regress into ever larger FS's as you pursue the chimera.
Weirdly enough, as Gentzen showed, you can use a theory that is "sideways" to first-order logic, neither strictly more powerful nor weaker nor equivalent in power, to demonstrate the consistency of first-order logic. Strong normalization theorems are used for typed lambda calculi like the Calculus of Inductive Constructions to show consistency, as well.
Unfortunately, it is sometimes the case that the remaining unprovable part is the most epistemologically dubious part.
See, for instance, "Coq in Coq", by Bruno Barras and Benjamin Werner, http://www.lix.polytechnique.fr/~barras/publi/coqincoq.pdf , in which the Calculus of Inductive Constructions is used to prove the consistency of the Calculus of Constructions.
It cannot be completely verified by Coq itself due to the Gödel theorem (well, now with this bug this is possible). Still, some part of it can be verified, like the byte-code interpreter. There is actually an ongoing project to make a certified JIT compiler for Coq: http://www.maximedenes.fr/download/coqonut.pdf