Cameron Bertuzzi of “Capturing Christianity” recently wrote an interesting post on the alleged conflict between skeptical theism and natural theology (i.e. arguments for God’s existence).
Undergirding the skeptical theist position is the idea that (on classical theism) God’s reasons for allowing and doing various things, especially in particular instances, are unknown. There are various forms of skeptical theism, and one of the most common formulations (as mentioned by Cameron) claims that our knowledge of goods and evils is not representative of all the goods and evils that there really are. Hence, the fact that we can’t see a good reason why God allows so much horrendous suffering, isn’t a reason to think that God doesn’t have a good reason.
One of the problems I have with Cameron’s post is the claim that if skeptical theism undermines arguments for God, then the effect is limited to only a few arguments like (inductive) arguments from fine-tuning. For instance, he says that a skeptical theist can:
… still affirm a whole host of arguments (e.g., the Kalam Cosmological Argument, the Contingency Argument, Craig’s deductive version of the Fine-Tuning Argument, the Moral Argument, the Ontological Argument, Plantinga’s argument from knowledge and proper function, and many others).
First off, it’s not clear that all types of skeptical theists can run these arguments. For example, the type of skeptical theism employed by Peter Van Inwagen  looks, at first glance, to be in conflict with running the ontological argument and the argument from contingency. In addition, one can run cosmological arguments that are inductive, and it’s far from clear why these would be immune from skeptical theism, including the version of skeptical theism that Cameron signs up to.
Secondly, if skeptical theism entails global skepticism, then skeptical theism indirectly undercuts all of the arguments from natural theology. One of the most common objections to skeptical theism is that it leads to global skepticism concerning knowledge, so that does seem to be relevant to the issue at hand since knowledge of God (via arguments) would be included in our “global knowledge”.
Thirdly, it’s not obviously true that the problem (of affirming skeptical theism and natural theology) wouldn’t impact Plantinga’s argument from knowledge and proper function, as pointed out by Justin McBrayer (who is a skeptical theist!).
Fourthly, at face value, skeptical theism would seem to potentially undermine arguments for Christianity. Take the argument from the resurrection. I can’t see a reason why God would start a false religion in the form of Christianity by resurrecting Jesus. But, that’s because (per skeptical theism) the goods that I know of aren’t representative of the goods that there really are. 
It’s far from obvious that if skeptical theism is true, then skeptical theism does not undercut most/all arguments for God’s existence. In fact, at first glance, skeptical theism seems to undercut the majority of arguments for God’s existence. 
Cameron briefly seems to hint that he thinks the problem of divine hiddenness is just an instance of the problem of evil, but he never specifies why he thinks this.
Cameron overstates the degree to which the argument from fine-tuning (if sound) confirms theism over naturalism. That’s because on theism there is an almost infinite number of universes for God to design. In addition, even though one might think that the mere existence of life makes theism more likely than it would have been otherwise, one must also ask to what degree does human life confirm/disconfirm theism. To ignore the latter is to commit the fallacy of understated evidence.