Well, Flag Counter doesn't list only independent countries in their list of countries. They include independent countries and dependent territories. Although Kosovo's sovereignty is disputed, it have more elements of independent country than some other entities that are listed. An interesting read about the elements of Kosovo's independence is this article...
http://geography.about.com/od/specificplacesofinterest/a/kosovoindependence.htm

Compare that to Taiwan's situation, which is already listed...
http://geography.about.com/od/politicalgeography/a/taiwancountry.htm

And a more general overview about criteria for country to be regarded as independent state...
http://geography.about.com/cs/politicalgeog/a/statenation.htm