Miracles and inductive inference
Atheists and these alike are both affected by the problem of induction. Frustratingly, there's no rational reason to think that the future will look like the best. The reason we do have the idea that it will, to use Hume's term, is merely the result of habit and custom. We all assume the future will resemble the past or what's known as the uniformity of nature.
If it wasn't for the uniformity of nature, all our inferences would turn out to be false; as it is, only some of them do. We suppositionalists insist that something is necessary to account for the uniformity of nature, and of course, God is invoked to do the job. On this view, God maintains the uniformity of nature. As an alternative, an atheist presupposition might simply be that the universe exists and that uniformity is part of its nature. In fact, it has to be because otherwise we wouldn't be here talking about it.
As it stands, both the theist and the atheist worldviews can be said to account for the uniformity of nature, but there's a complication. On the theist's worldview, there is a God who performs miracles. Miracles are amazing events that we would not normally expect to happen. In fact, miracles, by their very nature, are events we would only expect if God had somehow let us know in advance that He was about to perform one.
The theist doesn't claim to know God's mind or what God's plans are, and he doesn't claim to be able to predict where or when the next miracle will occur. This is important because it means that the next time the theist drops a pen, he can't say whether or not a miracle will prevent it from falling to the floor.
At this point, the theist might object that this is a silly example and God isn't in the business of performing silly tricks like that. Each of God's miracles, in fact, makes sense and is for something; it is part of a greater scheme. But the problem remains because even if, sorry, because if you don't know God's mind, you can't rule out the possibility that God might have a very good reason for preventing the pen from dropping to the floor that you're not aware of.
Both the atheist and the theist might be surprised by the way nature works from time to time, and their inductive inferences will turn out to be wrong sometimes, like in the example of the black swan. But the difference is that the theist worldview explicitly includes a magical being who can make amazing things happen by an act of will.
So, to make any particular inference, an atheist just needs to trust that nature is uniform, but the theist has to trust that God will maintain the uniformity of nature, and he has to hope that God won't perform a miracle that confounds his prediction. A theist is intellectually honest; he has to admit that he's in a worse position to make an inductive inference than the atheist is.