Belgrade hasn't shown much reaction yet, but it will obviously see this as a direct slight by their neighbors. It is not like Serbia and Croatia are exactly best friends, but this is a strong statement by Croatia. Football maybe only a sport in some eyes, but its global popularity and financial value make it much more than that. In this case, where Croatia is further legitimizing the independence of Kosovo by sending its best soccer team in, the game has political significance. Serbia does not recognize the independence of Kosovo, nor is it going to any time soon, and thus seeing its neighbor to the north make such a clear statement of its own, which is in direct opposition to Serbia, is a studs up diplomatic tackle.
What is the motivation for Croatia in all this?, would be the key question. Politically it is clear that Croatia is working hard to get a spot in the EU, and since 22 of the 27 EU states have recognized Kosovo, it is fairly clear that Croatia is following the trend (the same argument can be made for Montenegro and FYROM by the way). Croatia is gaining some bonus points by engaging with Kosovo on the civic level, as well as on the political and the economic. But I think one needs to look deeper than that as this is also a move to shore up internal support for the Nationalistic government currently in power in Croatia.
Croatia has benefited in the past from taking aim, literally and figuratively, at Serbia. Likewise, Serbia has done the same to Croatia and benefited as a result. During the 1990's the Tujman and Milosevic regimes were rather complementary in achieving their designs for the territory of Yugoslavia. Their vicious brands of Nationalism, Leftist in Serbia, and Rightist in Croatia, enabled them to mobilize their people to break free from Yugoslavia and from each other, and to make their claims over Bosnian territory. So while they were in direct conflict with each other, they were actually helping each other at the same time.
While the context is different now, and there is less perceivable benefit for Serbia in this, beyond what Carl Schmitt would argue is giving Serbia a clear enemy against which to define itself, Croatia can marginalize its own Serbian minority from the political and cultural sphere, keep the nationalists happy by poking Serbia in the eye, and please Europeans by being a nice brother to little Kosovo. This also serves the American agenda that, for very unclear reasons, seeks to keep Serbia down. Having regional actors, especially such 'clean' ones as Croatia (an image not at all justified) engaging with Kosovo only blosters the inevitability of its de jur status as a Nation-State.
So football has a clear political agenda here. It serves Croatia in sprucing up its image abroad and in securing support back home; it serves Kosovo because it gives legitimacy to the institutions (such as the Kosovo Football Federation) and the government itself; and it serves the Pro-Kosovo international community in legitimizing its bid for statehood.
