"Why was it "not a popular statement to make?"
Because the Upstate GOP wanted Rudy's head on a platter for it.
Naturally, they forgot all about it when it came to running Rudy against Hillary for Senate, but I guess their change of heart then was a principled stand rather than a matter of convenience (beat Hillary at all costs), huh?
OK -- so it was popular among people who actually lived in his jurisdiction and unpopular among people who lived outside it (and therefore had no say in his prospects for re-election).
I don't think this has anything to do with "convenience" or "political stands" -- but has everything to do with basic political opportunism.