Well, I can only answer your question for myself, Kappa.
I guess there are people from both countries that hate each other, but I think that they are minority. Even though I don't agree with Croatian politics (but I also know, that our politicians are no angels either), I have no reason to hate Croats just because they are Croats or because we once lived in the same country and no, I don't hate them. Why would I, they have done no harm to me. If I was to hate someone, I would because he/she was an evil character, not because of his/her nationality/race/religion.
Of course, speaking in football terms, there is a huge rivalry between our sides. I guess it's more on our side, since we more like to compare our teams to theirs, who have usually been more successful over the years. Also, I still remember Alen Boksic (former Croatian NT), when asked who is the most dangerous Slovenian player, saying: "Bojan Krizaj", who was our most famous skier (and thus implying, that we are only good for skiing and not for football) - I guess this joke (afterwards, he said it was only a joke
) contributed a great deal to the motivation of our NT, when playing against Croatia and they always had hard time playing against us, even when they were at their peak and we were still a sh!tty team.
And yes, some lunatic hooligans will probably smash a car or two during these matches, but I am sure there are very few on both sides, who will actually approve their behaviour. I don't think there is hatred between a population of the two nations, at least not in general. We may not be the best buddies out there, but hatred - no.