Well, Milosevic's "original sin" was that he was a socialist who resisted the West's push (led mainly by Germany and the US) for the breakup of Yugoslavia as far back as 1989. He didn't want to subject Yugoslavia to the painful economic reforms of privatization, strict IMF rules, etc. that were afflicting so many of the other former Eastern-Bloc countries under communist rule.
Because of his resistance to the West, the western media painted the conflicts in the Balkans as a war of good (The Muslims) against evil (The Serbs). As such, and with strong media support, it was easy for the Clinton administration to stigmatize Serbia as a rogue nation. Unfortunately, we're still paying the price for this negative stigmatization.
You said it all!
While you are correct about the Western media choosing sides, you are wrong about the reason why.
The media chose to portray the Serbs as evil because many of them are Christians (of course, the Communists among them most often were not) and the Muhammedans certainly were not. If it's Christians vs. non-Christians, the Western media will always support the non-Christians.
They vilified Milosevic because he was a Serb, not because he was a Communist. Just look at how the Western media stands on its head to avoid ever saying anything bad about Castro and you'll see what I mean.
The Western media, being dominated by socialists, communists, homosexuals and atheists should have taken a liking to Milosovic for being a socialist.
I think the Western media tends to paint good as bad and bad as good because their agenda is to take down Christian nations and whatever goodness they stand for, no matter what the means --- even if it means allying themselves with the Islamofacists. If you look very, very closely at the media, it is Christianity that they fear and hate the most.