It's everywhere. I grew up in Upstate NY. Outside of the cities it's a fairly rural and backwoods area, and I went to high school with a lot of people who would have confederate flag decals or actual flags. Whenever I go home I'll still see some sort of confederate symbol. You live in the north, in the middle of NY. How do you have any connection or sympathy with the confederacy.
The ante-bellum South has a tendency to be idealized in, it seems, thousands of different ways. On one hand, there is the state's rights side of it. There can also (rather accurately) be a sense of the Civil War as a conflict between rural agriculture and urban industry, which I think accounts for the New York phenomenon you mentioned. Further, the South of books like Gone With the Wind certainly has admirable qualities. On the other hand, the ante-bellum South can also be presented as a Hell full of demonic white racists. Of course, no such idealized portrait is actually right and none of these portrayals was actually limited to the South, but people can tend to be drawn to one they can relate too, and develop a relationship with it from there.