It would be funny if it weren't more optimistic than the theology in question...
Okay, ready? So, the literal reason I find this funny is the notion that god, as envisioned by most monotheistic religions, might essentially have made a straight up statistical error. If you look at the means- life spans are getting longer, crime rates are going down, happiness is generally increasing- on the whole, it looks like a pretty good world. Once you start paying attention to the dispersion, however, suddenly things snap into a different kind of focus. It's a useful way of pointing out that the story we tell can in many instances depend on what data we're paying attention to, and if you're not paying attention to all of the relevant data, you're probably missing something.
The implied reason is that frame at the end where the priest deals with the situation by explaining that god works in mysterious ways. He knows the reason for evil now, the holy grail* of theodicy, is simply that while god is all powerful and all knowing he isn't always paying attention to all of that knowledge. I suppose you could claim that this violates the "all knowing" clause, but omniscience doesn't necessarily have to imply omni-awareness, does it? You can know something without necessarily thinking about it, so maybe the answer to the problem of evil is simply that god just isn't paying any attention, or isn't paying enough attention. But, this answer isn't going to be satisfactory to the flock, not least because it's an insanely humbling notion, and so we get that hoary old chestnut about mysterious ways instead.
The unstated but depressing reason I find this funny, however, is that it actually deviates from one of the key elements of Christian theology: the fall. See, the notion is that before Adam and Eve ate from the tree of knowledge, everything was awesome. Afterwards, however, they were cast out of paradise and things generally went to shit. Moreover, a large number of Christian denominations have basically taken the stance that the world is gradually getting worse, and will continue to do so until Jesus returns. There's great in-character discussion of this in Umberto Eco's The Name of the Rose, but for a modern example just hang out on Conservapedia for a while.** So, in short, this is both funny and sad to me because the very notion that god would resolve the problem of evil by explaining that things are actually getting better is, itself, fantastically heretical.
And that's depressing because in the midst of a presidential primary process that features repeated and aggressive claims to be more Christian than one's rivals, the notion that Christianity asserts that things can't get better is just awful.
* Pun intended.
** Particularly see #2 under Biology in this article.