Nova Scotia was the first colony in the British Empire to be granted responsible government (i.e. democracy), and felt a certain distinctness from the rest of British North America. In Canada's first election, Nova Scotia elected overwhelmingly anti-Confederation politicians, and petitioned the British government to allow separation from the Dominion of Canada as a separate colony/political entity. The British refused to let them separate, and that was more or less the end of it.
Manitoba also saw the Red River Rebellion and the North-West Rebellion led by Louis Riel to protect Metis rights, and allow entrance of Manitoba into Canada on its own terms, rather than being dictated terms by the predominantly Anglophone government in Ottawa. Although there were some calls for a republic, the Metis and Francophones in Manitoba weren't necessarily opposed to Confederation as they were opposed to how it was done.
A more contemporary example would be the Quebec separatist movement of the late 20th century and its retroactive opposition to Confederation.