The major cause of unrest in the backcountry in this time period was discontent with the performance of the colonial governments. The colonial governments were run by elites from the coasts and the backcountry people felt that these elites were insenstive to their needs.
Most importantly, the backcountry people wanted to be protected. They were living on the frontier where they faced threats from Indians and outlaws. They wanted the government to do more to protect them. When this did not happen, rebellions like that of the Paxton Boys in Pennsylvania took place.
In addition, backcountry people sometimes felt cheated and abused by the coastal elites. They felt that the government was acting in ways that helped the rich at the expense of the backcountry farmers. This sort of complaint led, for example, to the "Regulator" movement in North Carolina.