Well, in all fairness, it wasn't about jihad alone, but it wasn't about secularism all alone, either. He started with an analysis of Islam's rejection of reason, support for coerced conversion, and different concept of God ("who could just as easily order idol worship"), and asked Muslims and other religions to dialogue on the basis of honesty about their positions.
It should be, as many have said, a golden opportunity for Islam to show that, contrary to 1400 years of appearances, it is not violent and repressive at root and core; but instead, it is determined to run forth and prove that it richly deserves all the negative things said about it.
The Pope's address was categorically not about Islam.
It's purpose was to address the divorce of theology from the university environment, and his belief that those two "cultures" had to engage in dialogue.