The origin of the word "nation" refers to the ethnicity (a folk, if you will) of the people that live in a land. No nation, no people. Example: The Roma, for example, are a nation without a country.

Now, to take pride in a thing means to regard it as good, worthy, admirable.

To take pride in one’s nation simply means to recognize the good, and to value, preserve, defend, and contribute to it. It means regarding one’s people, heritage, and public order as worthy of loyalty, care, and continuation. It does not require the claim that one’s nation is perfect, nor that it is superior to all others.

Nationalism becomes problematic as soon as loyalty to one’s own people or country becomes more important than truth, justice, and proportion. I think that there is where the issue truly lies.

TL;DR: There is nothing wrong in recognizing the good your nation does, and recognize that another nation may be incompatible with yours in certain parts is OK. "Abusus non tollit usum" - Cicero (I think?): "abuse does not cancel use", or "misuse of something is no argument against its proper use".