Don't know if you would consider these big cities, but it was either Charleston, SC or Savannah, GA where they were very clear to point out that they didn't have a local Chabad--and were very happy about the fact! For whatever good Chabad does in far-flung places, they sometimes are unwelcome in less far-flung places because they draw from an already small community, and can divide the community. Even here in New Hyde Park, where Chabad has a house to house and feed family of hospital patients at LIJ, the local Young Israel is pretty pleased that Chabad does not have a shabbos minyan.
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