I'd like to think that the newer generations would get along better, but it really depends how they're raised and the opinions of others that surround them as they grow up. More than likely some will and some won't. But I must say, I don't envy NI with the scars it has to bear from the troubles.
It was probably more comparable with the Israel-Palestine situation formerly, but now, from an outside perspective, it seems mostly over. So perhaps it's a bit like parts of the former Yugoslavia, where it's time to pick up the pieces and try to heal? To be honest, I don't know, but that's how it seems to me. Unfortunately, I'm not sure the religious hate will fully go away for quite some time, as much as the teachings include forgiveness, religious animosities rarely die down quick, if at all. I mean look at the Catholic-Orthodox schism, still not fully healed after more than a millennia. Seriously.