I think in this case, the story is more about Apple's disregard for the spirit of the court order than being down on Apple in general. I'm generally an Apple fan, but this seems kind of petty and oddly antagonistic towards the court.
If they were truly told to write an apology, then people are down on them because this isn't one. You cannot really apologise for anything without using the words 'sorry' or 'apologise'.
I agree with you - but I've read in several places that Apple were ordered to apologise. Their feelings (or not) don't come into it.
[BTW - the linked text kind of implies that they do have feelings; the article comes off as surly, resentful and not a little childish...]
[EDIT: Seems like they were never actually ordered to apologise, only to clarify that Samsung did not, in the judgment of the court, infringe on anything.]