Briefly, the article is about why evolution and theology might not be incompatible, and that both the religious and the non-religious might understand this better if they understood the evolutionary algorithm (his phrasing) to be more powerful a process than they currently do.
Its an interesting article because it is written very much from an algorithmic perspective. In addition to referring to evolution as an algorithm (which is great!), Wright focuses on human morality as an illustrative example: he claims that morality is a sticking point between the religious and the scientific: Extremists on one side take the existence of a universal human moral code as proof of the existence of God, and as something that is incompatible with Darwin's theory of evolution. Extremists on the other side take evolution to justify moral relativism, to believe that morality is a quirk of human evolution, and not universal or "true" in any sense.
Wright gives a nice summary of the argument that human morality can be explained as a mechanism to allow people to play non-zero-sum games. On the one hand, we feel badly about betraying others, and on the other hand, have an urge to punish those that have betrayed us. This is exactly the incentive system that is necessary to play repeated prisoner's dilemma at the socially optimal equilibrium, and when put this way, seems like a perfectly reasonable outcome for an evolutionary process.
So a moral code provides an algorithm to play a repeated game. Now Wright supposes that we might live in a nicely behaved world, in which there exists some unique algorithm that is optimal in repeated self play. And perhaps it can always be found with local search. And perhaps we've already got an epsilon-approximation to the optimal moral code. (I am now deviating a bit from his exposition... But this is basically what he is supposing. It is in these assumptions that his argument is weakest.) If you believe all that, then given enough time, the evolutionary algorithm will always produce a species with the same moral code.
In this case, the argument for moral relativism goes out the window. Human morality isn't arbitrary, it is optimal, and in that sense, it exists "out there" as a universal truth independent of humanity. On the other side of the coin, if you believe that evolution is an algorithm which is guaranteed to result in the true moral code inscribed by God, because morality yields a survival advantage, then you can better believe that God created life merely by beginning the process of evolution. He could do this with certainty that it would converge to the optimal solution, which he designed by setting out the initial conditions.
Ok, so its a philosophical argument that has been rehashed over and over again, and isn't going to convince anybody of anything. But its nice to hear it rehashed as viewed through the algorithmic lens.