I think one of the reasons for the Judge ordering the advertisements is because of the way Apple's legal council blatantly accused Samsung of copying the the iPad. Since the court proceedings and what was said in them were publicly quoted, the accusations by Apple's legal team were seen as a public accusation, which was found to be wrong, hence the need for Apple to publicly retract it's comments.
Had Apple's legal teem been more circumspect in their language and conduct, the advertisements likely would not have been ordered.
Apple can't just put the advertisements on their website, they have to take them out in several major national newspapers as well.
So if the Police charge someone in the UK with an offence and they are later found not guilty, then the police have to publish an apology in the major national newspapers and on their websites?