He only apologized for the ruckus it caused. He didn't apologize for saying it.
Let's take a look at that apology again:
"I am deeply sorry for the reactions in some countries to a few passages of my address at the University of Regensburg, which were considered offensive to the sensibility of Muslims. These in fact were a quotation from a medieval text, which do not in any way express my personal thought. I hope this serves to appease hearts and to clarify the true meaning of my address, which in its totality was and is an invitation to frank and sincere dialogue, with mutual respect."