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Let's review few logical points from the article:

If God endorses Islam, the truth, and its expansion by His sovereignty and compassion into non-Muslim lands in order to show God’s will (shari’ah) to pagans and people of the Book (Jews and Christians, then it should be able to expand endlessly and cover the whole world with His truth.
God does indeed endorse it, according to received theology; therefore, the rest follows logically (the consequent necessarily obtains) -- ole fashioned modus ponens (affirming the antecedent):
1. If A (antecedent), then B (consequent).
2. A (the antecedent is affirmed).
3. Therefore, B (the consequent follows necessarily).
Such must be the psychological expectation of observant, concerned Muslims who care about Islam’s spread, and especially of fanatical Muslims. Thus, theology and logic worked harmoniously, so Muslims did not experience cognitive dissonance or shame—in the distant past.

and further below:

Consequently, history in the last three or so hundred years teaches not-B, so the old, positive logic must give way to a new, negative one. Briefly, the new logic says that if God endorses Islam, then it should expand endlessly. However, it is not expanding endlessly, but receding in the face of the expansion of the West, the “Christian” lands. The new conclusion must be terrifying to violent fanatics, but it is they who have initiated belief in the first two premises. The conclusion: therefore, God does not endorse Islam. This is known as modus tollens (denying the consequent):
1. If A, then B.
2. Not-B (the consequent is denied).
3. Therefore, not-A (the antecedent is also denied).
For fanatical Muslims, the internal (psychological expectations) and the external (historical reality) are in conflict. Therefore, they are experiencing cognitive (religious) dissonance as they work out the simple, terrifying logic.
...Basic psychology says that a subject experiencing cognitive dissonance (and presumably shame) may do the following: (1) alter one of the dissonant cognitions; (2) reduce the importance of one of the dissonance; or (3) add new information that reconciles the dissonance.

and he finishes the article with this:

Clarity brings resolve: first, more Westerners must understand the one deep motive of the violent fanatics. Second, in order to teach them that their theology is twisted and that God is not on their side, more Westerners must therefore join the fight to eliminate them before the terrorists eliminate or paralyze Westerners over the next several decades.

How about we help to increase the dissonance to further prove the falsity of A. Destroy Mecca and Medina and simultaneously blanket the Muslim world with radio, TV, paper flyers assaults claiming exactly that: "we will not be punished by Allah, therefore he is not great. At best, you, Muslims, are mistaken in interpreting his will of conquest. Deal with it, wipe out humiliation and join the world community. End of message" That what our ancestors would had done if they could. We can. (Will we? I don't think so, unless they explode a nuke here, nothing less than that. Even then I am not sure we'd do it).

Allah FUBAR!