'Rise' and the fall of anti-racism
http://www.boriswatch.co.uk/2008/06/15/rise-and-fall-of-anti-racism/
FWIW I think you could argue that rock's hatred/contempt/fear of hip-hop stems in part from resentment at its success; the fact that since the 80s black musicians - thinking more of america, but it applies here - have succeeded in dominating the charts. Albeit of course the usual caveats about middle aged white men still pulling the strings apply.
I think a lot of rock/metal fans see themselves as operating outside of the mainstream, or in opposition to it- hence hilarious ''you laugh at me because i'm different, i laugh at you because YOU'RE ALL THE SAME'' t-shirts and a general attitude of hatred and contempt towards pop stars and, yes, hip-hop stars (of a certain kind). To be honest I think there are quite a few hip-hop acts that wouldn't get bottled at Reading and maybe not even at Download- The Roots, Jurassic 5 etc.
50 Cent got bottled at least partly because of the image he projects of himself (gangster, obsessed with making money, shooting people, treating women like shit etc.) seeming to come into conflict with how rock fans see themselves (anti-establishment, anti-profit etc etc.) Funnily enough I can't imagine Jay-Z getting bottled at Reading (maybe because of the Linkin Park connection?), though.
Tribalism is definitely another element- 50 Cent also got bottled because he seemingly represents mainstream pop culture. I remember going to Deconstruction years ago (a ''punk'' festival, where most of the acts sounded like New Found Glory i.e. not remotely punk at all) and Lost Prophets got showered in piss bottles because they were perceived as not being ''punk'' and therefore not belonging there.
On the other hand, sometimes I think people are just perceived as being shit. I remember having a good chuckle at Good Charlotte getting bottled at another Reading, and you'd have thought they would go down a storm, wouldn't you? I suppose they are perceived, again, as an MTV version of punk i.e. fake and corporate. But it must partly have been down to the fact that people think they are shit.
As for racism- I don't think that's necessarily a huge motivating factor behind this. There's bound to be a minority of idiots in a festival crowd that big and that volatile, especially at a festival dedicated to music that is, at times, massively aggressive and committed causing offence. The person who threw that banana was probably a teenager with a pea for a brain.
Some people just hate rap music, it rubs them the wrong way. They don't like the attitude in it, they don't like the posturing, they don't understand it... I don't think Noel Gallagher was being racist with the whole Jay-Z thing, I just think he's musically small minded.