IIRC this man is an atheist. He's at a genius level, that he studies and writes a lot about religion. Among other things
http://chronicle.com/jobs/2005/01/2005010701c.htm
His use of the term "theocrat" tells you all you need to know. Christians are not "theocrats," but Stanley Fish likes to consider them such and spread his fog of moral equivalency over the situation. Islam, on the other hand, is truly theocratic, and is probably the only existing truly theocratic system: it believes that religion and politics, religious and political governance, are one and the same and are to be executed by the same persons. Even a country that establishes a state church or a country like Israel, that is officially Jewish, is not the same as a theocracy.
You will note that the "secularists" everywhere - in the media and in left-wing politics - are on the side of Islam. So that should be an indicator that the situation is much more complex than Fish likes to admit, and that religion is not a very explanatory word, since it can cover things from cults where you offer your children to Moloch to religious orders where you go off to die working among the lepers.
I think the Pope was trying to establish the actual grounds of the conflict, which is between reason and nihilism. Christianity is based on a reasonable view of the universe, which came to us through God's revelation to the Jews and the philosophical foundations of the Greeks that are expressed in the New Testament. Islam is fundamentally irrational and has a concept of a god who is arbitrary and irrational and bound by no interior consistency, and who can be known only through his draconian laws. Oddly enough, secularism has the same view of an irrational, meaningless universe, which runs on laws somehow mysteriously produced and imposed by matter itself, but which also is fundamentally without a purpose or rational direction. So I think perhaps that's why the devotees of the left and the followers of Mohammed get along so well, because they are both nihilists at heart.
Stanley Fish has been published 4 times in Frontpage magazine. So conservatives like some of what he says
http://frontpagemag.com/Articles/authors.asp?ID=1244