'protection' was a policy introduced in 1938 by the British Parliament and applied to the Aboriginal people. It was basically to protect, by isolation, from violence, disease. But also allowed the government to acquire even more land, because it went hand in hand with the missionary activity.
assimilation is a 19th century idea that aboriginal people should be 'improved' by being 'civilised' and Christianised. From the 1930s, assimliation was government policy and in the 1950s legislation was introduced to enforce it. The ultimate aim of this legislation was the eventual destruction of Aboriginal society through the 'dispersal' of individuals and the breaking-up of Aboriginal communities.
so basically assimilation sought to breed out and destroy the aboriginal culture. Whereas the protection policy is looking at a different aspect, to isolate the Aboriginal people for their own protection from the white people as well as so that the white people could get some benefit from the policy.