A solid question.
Based on The Tempest, I would say that Shakespeare thought that colonization was potentially dangerous and wrong thing, but that he wasn't deeply concerned with it, and that in fact he saw some reasons for it. I base this on two things. The recognition of the potential harm of the practice can be seen in Caliban's response. Showing Caliban's pain and anger at Prospero's rule shows at least an openness to listening to the cries of the oppressed. However, Caliban is also shown as drunken and foolish, and in need of someone to rule him. Therefore, while Shakespeare sees the risk, he's not automatically opposed to it.