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As you know, "藉贯”means the birthplace of oneself but "祖藉" means the place of living of one's ancestors, so when someone says “我的祖国”, does he mean the country of his ancestors or the country of his own (for example, he is an American Chinese born and living in the US)?
The latest edition of 新华字典 says that 祖国 is the country of one's own(对自己国家的亲切称呼）（Page 674,新华字典第11版，商务印书馆，2012）, so it is very confusing, what does 祖 here mean?
祖 generally means ancestor, 祖国 means someone's own country and MAY have the implication that his/her ancestors lived in the same country as well, although it doesn't always have to be the case. I think 祖国 is similar to "motherland" in English, an expression to imply close relation. As an analogy, although "mother" and "land" give you a feeling what the word "motherland" means, being really serious about the meaning of "mother" itself won't help much here.
P.S. As a Chinese, I usually perceive Chinese words as a whole rather than separating every character and studying them, but I'm not sure if this is the best way for learning Chinese as a foreign language.
By my native speaker instinct, 祖 is origin. 祖国 is the country where one comes from.
By my favorite online dictionary, 祖 means ancestor. 祖国 is the country of one's ancestors. - http://www.zdic.net/z/20/js/7956.htm
祖國 probably imported along with nationalism from Western world. You can find fatherland, vaderland, vaterland and many others in European languages.
Imperial China is the centre of the world, containing vast of piece of lands. It is no need to use the term "ancestor country". People under imperial China is clan-oriented, not country-oriented. Instead, they preferred to say their home "village" and "county" (not country!), and places where ancestors lived. This is why people refers to 祖藉 instead of 祖國.
In common speech, 鄉下 is more frequently used. Even if one goes out of China, they refers China as 唐山.
It is better not to use 祖國 as it has nationalism context. It is widely used in propaganda.
祖国 would mean the country of one's ancestors, rather literally，and this is how it is usually used in my experience. It does have some nationalistic connotations, but these are not necessarily negative. It's all about what you're discussing, and context, after all.
祖 is composed from spirit(left) and penis(right). So the meaning is "ancestry" or more precisely - "fatherhood", which are related with the above mentioned parts. Now 祖国 should mean "Contry of fathers" or "fatherland".
