Pope Benedict did not apologize for what he said but for the conesequences of what he said. It’s not surprising that some Muslim leaders want a more unequivocal papal statment.
However, there may be less here than meets the eye. The statement the Pope quoted from a Byzantine emperor condeming Muslims was inserted into a thesis type presentation. It could almost be construed as adversarial to the point the Pope was making, ie that all religion should be pacific. Considering the context, it is difficult to see what more the pope can say. However, as Barbara points out in her second comment, the academic in Benedict can not longer engage in public hypothese without risking that he will be misunderstood.