I agree with you. There are many pretty good countries and they all have what I'll call rickets on some matters, and within them detractors for good reasons.
Or bad reasons. And what I might think is a pretty good country might not fit with another person's opinion across the globe.
I do think a lot of people everywhere who are even aware of the nature of the country they live in (compared, say, to their village) have a wish to like it and think it is best.. it seems natural to me. So does people hating a particular regime seem natural to me, and some of those people protesting may be feeling that way for love (effectively) of their home area, wishing to protect it.
I'm not a fan of constant jingoism, which I feel edges into nationalism - but I'm fine with being not only a fan but a booster of where any of us may live. It is a kind of attachment. Personally, I've moved several times in my life, but I still have attachment to the old places.
Haven't read the New Yorker article, but will, thanks for the link.