Not all of the violence. The fight scenes were significantly amped up. For example, in the comic when Dan and Laurie get mugged, they pretty much just punch out the attackers, and Laurie breaks one of their noses. In the movie there are close-ups of bone splinters being forced out of skin (actually, the movie seemed to have a lot of bone splinters). The death of The Comedian is a pretty short flashback scene in the comic, while in the movie it was turned into an extended brawl. The fat prisoner's throat is slit in the comic, and it cuts away to show Rorschach's impassive face as it happens, while in the movie his hands are cut off with a circular saw in full view of the camera with blood spraying everywhere.
I liked the movie, but they definitely amped up the violence, almost into gore-porn levels.
You're right, though, that a faithful adaptation of Watchmen could not be PG-13.