Yes, yes yes, we all know that monkey can be used affectionately. But I'll give you some hypothetical situations involving two made up people, we'll call them Kevin and Colin.
1. Colin is sporting a new haircut and Kevin makes a joke at his expense, Colin calls Kevin a "Cheeky Monkey". Result (apart from wondering why they are talking like 12yo's) is Smiles all round.
2. Kevin is helping Colin stack some tins of paint, Kevin is messing around and knocks them over. Colin calls Kevin a "Bloody Monkey". Result - Kevin learns a valuable lesson, don't muck around while helping Colin, but no harm is done.
3. Kevin and Colin are in the pub and have had one or two beers. Kevin happens to be black. Kevin starts telling Colin that Everton are rubbish. Colin tells Kevin "Shut Up You Monkey". Result - Kevin smacks Colin in the face.
Now I simply refuse that anyone with even half a brain can't see that the third example is racist while the first two aren't.