Each course of actions has its advantages and disadvantages, and taking a different tact on repeat playthroughs can yield slightly different gameplay experiences. You're free to choose whether or not to play nice or conquer them in battle.
You'll also come across other European colonists seeking to establish their own settlements in the newly trodden territory. Others will not take kindly to your trespass into their region, sparking wars in the process.
Some native tribes will welcome you as best pals with open arms and can prove to be useful allies.