Lets forget about he NCAA violations and get back to the basic question the OP stated; why do people hate Rupp.
The answer is this: He gets benefits most pro runners don't even receive. He gets these benefits from the biggest athletic corporation while an 'amauter' NCAA student athlete. The benefits he receives are ones that no other college athlete has a chance to receive.
Having the backing of Nike while in College is sketchy enough for me.
For the person who posted above me talking about the indoor track. It's not as simple as 'I have a indoor track right near my house I should run fast too'. Think about this;
You are a top 15 type NCAA XC guy. If a guy finishing near you has access to things you cannot even receive, train to get, buy or your team cannot get how would you feel? Would you consider that person to be a cheat?
Rupp has access to Nike's training facilities ie; state of the art anti gravity treadmills, world class training partners, recovery systems in the form of massages, doctors, training tools, altitude tents/houses, etc. All these things are not funded by his University, rather NIKE. Amauter? I don't think so.