Example: On reddit there was an article about a boy who ordered McDonald's and ate it at the scene of the fatal accident he had caused. Later it was reported he had fled police custody and on the news site that reported this, a McDonald's commercial was featured prominently.
http://i34.tinypic.com/20ifms7.jpg
While seemingly inappropriate (and funny), it in no way reflects on the McDonald's brand.
Even if the case was Justin.tv and Nike:Just do it, I think that most people are sensible enough to see that it's just a case of coincidence.
Anyone who gets seriously offended or angry in these cases is most likely trolling for attention or is completely clueless as to how advertising works on the internet.
"wipe billions off the value of a brand"... really? come on!