It think it's a mistake to put all nationalisms in the same basket. It's a mistake to say they're all good or all bad. I think some are good and some are bad. If you feel good and you care about where you come from or where you live, that's good. If you start to hate, attack and try to get on top of anybody else, that's when nationalism becomes a problem.
The European Union has the potential of being a good thing. But if the deal goes all wrong, if some powerful global financial interests put way too much weight in the balance, some nations might feel left out. Some nations might feel they have too much to lose in the EU, they might ask for some major change or even want to leave the Union all together.
In some cases, no deal at all may be better than a bad deal. For example, I'm a Quebec separatist. I think that Quebec would be far better off as a country of its own than to remain one of the ten provinces of the Canadian confederation. It doesn't mean that we hate the rest of the world and that we want to clamp down on ourselves. We just want a better kind our relationship with our neighbors and the rest of the world.