It wasn't just an Albanian flag. It was the Albanian flag over a map of Great Albania, which includes territories of almost all Albania's neighboring countries. If you have in mind that only 15 years ago Serbia and Belgrade were bombed by NATO over this (Kosovo) and if you try to understand the Serbian emotions over losing Kosovo, you might understand the anger of the people there.
This is like playing a Muslim country, and a drone flies over with a picture of Mohammed touching himself while watching a photo of Justin Bieber. Or playing Israel and a photo of Hitler flies over the stadium in Tel Aviv.
The anger of the people in the stadium was understandable. What should be judged is the reaction of the players who attacked the Serb that put down the "flag", and, of course, the failure of the security to stop the fans from entering the stadium.