Consider the virtue of patience. I think it is clear that it is reasonable to be patient. But certain forms of patience are not reasonable, if naturalism is true. On naturalism, I can be patient in line at the store, or with other drivers, or with my children, because of the therapeutic and relational value of patience in these realms. However, the naturalist cannot as easily account for the patient endurance of suffering or trials, in the following way. What am I waiting for, in the midst of terminal illness, challenging trials and tribulations, or an apparently irresolvable situation, when the desired states of affairs are outside of my ability to bring about? On naturalism I’m waiting for “my luck to change” or something along those lines (and whatever that means). This seems to be a weak basis for patience, and not a good reason to think that whatever I am waiting for will in fact occur. On naturalism, the attitude is “Wait and see.” By contrast, on theism I am waiting for God to come through. The attitude is not merely wait and see, but rather “Wait and see how God will prove his faithfulness.” For the theist there are positive reasons for patience, for expecting something good, sooner or later, to happen. There are reasons to be hopeful in patience. This is not the case on naturalism, making patience in many contexts, for the naturalist, irrational.I suppose the "naturalist" could just accept this, and say, sure, there will be points at which there remains no reasonable ground for hope or patience. (I will not worry too much here about how Mike may be running hope and patience together here; I agree that patience only makes sense when there is room for hope of some sort.) What I want to object to is the implicit assumption that patience is passive--that it is just a kind of waiting for someone else (e.g. God) to do something or something else to occur (e.g. a turn of "luck"). I think we can also talk about being patient with oneself, and in the sort of case that Mike seems to think pose a problem for the naturalist--where great adversity must be endured--it might be argued that we sometimes need patience with ourselves, in terms of our current ways of understanding our own situation, in order to make room for other ways of seeing the situation that make it more bearable, or which allow us to see a (new) point in enduring. I don't just mean being patient until one is struck--either by divine grace or dumb luck--by the "silver lining." Rather, I mean the patience, roughly, to explore other possible ways of seeing the situation, and perhaps along with this a kind of hope that we can find a way--through our own creative thought, the example of others, and so forth--of making sense of our situation that gives us some reason to endure.
One could object--if naturalism is true, then there's no guarantee that this as-yet undiscovered perspective is "out there." The situation may indeed be hopeless. But there's also no guarantee that there isn't. One reason for patient endurance in the face of adversity is the possibility of learning some lesson, which may only be clear when and if one comes out the other side. And here, I would emphasize that patient endurance would only be one part of the story, since such endurance is renewed by the continued search for a meaning within the situation (i.e. by activity).
Of course, that reason seems moot when the affliction one faces is, as it were, "terminal"--what room for hope, and so patience, is left there? Here, perhaps the issue depends on what one thinks it means to die with dignity. Suicide might seem to be the cardinal sin against patience, particularly if one thinks that we should always wait for death to come to us. But given medical technology, and the ability to keep a brain-dead body alive long past any point of possible recovery, and the presumption that loss of autonomy can be completely psychologically overwhelming, such that it becomes impossible for a person to be an agent (and so to exhibit any virtue, let alone patience), I'm not sure that the decision to end one's life in some situations is the same thing as losing one's patience.
At any rate, the short story is that I think Mike is wrong to think that the naturalist is short on grounds for patience even in fairly incredible situations, in part because waiting needn't be waiting for something external to happen, but waiting--and working--for a shift in one's own perspective, the creative discovery of a reason, as Dylan Thomas put it, to rage against the dying of the light.