As a Kosovan Albanian, I don't like that analogy in the first place, neither I do the mentioning of genocide in Kosovo (in Bosna it is different). The Holocaust analogies really don't serve and are offending to the Jews. On the other hand, there were really massive war crimes, mostly from Serbia in the war of Kosovo.
Saying that, I genuinely do not see why on Earth that should be offending. It is hardly a symbol of war of Kosovo, it is hardly the symbol of Greater Albania, or some other myth. It is the symbol of Albanians (among others), and it is is in the flag of Albania, which among others it happens to be also in Belgrade, is Albanian's embassy. And in recent years, the relations between Serbia and the Republic of Albania have actually been quite good. If he had made the symbol of Kosovo (how on Earth can you do that in the first place), I could have understood the reaction, but that hardly wasn't the case.
Now fans and Serbian politicians getting offended is quite understandable considering that they love to be offended and finding the gesture provocative, but apparently Kolarov got offended too. He went as far as to call the Swiss players primitive, and to say that we aren't like them. Which kind of proves that he is a goldfish.
This happened after Serbia scored against Albania, in Albania:
Now the three finger sign originally wasn't meant to be a nationalist symbol (it is just the Holy trinity) but it had been used intensively from Serbian paramilitaries during Yugoslavian wars, so a lot of people might find it offensive. However, unlike in this case, no one really mentioned it, fans didn't throw things at the players, and Albanian's president didn't cry and say 'they hate us, but we are good people and we do not have anyone', neither players complained, neither Albanian manager wanted to send referee or someone in Hague.