The Great Compromise solved the problem of representation in Congress during the Constitutional Convention. There were two competing plans to decide representation in Congress. The first, the Virginia Plan, was to provide Congressional representation according to a state's population.
If colonists mistreated natives in any way, treating them as less than human, that would indeed inflame the native population, leading to increased tension between the two groups. This problem, when not solved, has led to revolts and few colonies.
