When you look at European colonization, certain places like Australia and the Americas were dealt with by slaughtering the natives, while in other places like India and the Philippines they didn't do that. Since genocide seemed to be extremely effective for the colonizing countries, why did they only do it certain places?
This question is pretty expansive, and given the more focused nature of AskHistorians you might have trouble attracting an answer. The nature of colonization was drastically different depending on time, place, and the peoples involved.
That said, there are, roughly, two ways to categorize European colonial projects:
More "settlement" oriented colonies. This mostly applies to the Americas and Australia, and this is where white settlers more or less exterminated and replaced local populations. Part of the reason this was possible was that native populations were decimated by disease and left disorganized, incapable of offering meaningful resistance to encroaching settlers. In this context, genocide was usually planned and executed by the settlers themselves instead of the mother country. Asking about Cuba or early 17th-18th british settlement of the future USA could get you a more in depth answer here.
"Extraction" oriented colonies. This dynamic is more relevant to sub-equatorial Africa and Asia, areas where large, organized, hierarchical populations were already extant. In these areas, colonization typically didnt involve large scale settlement, and instead Europeans in the colonies where typically more present as administrators, forming a top layer on the existing hierarchy. In these colonies, while killings of natives were widespread, full scale extermination and replacement of the population wasnt carried out for various reasons, though the most consistent was the fact that these (mostly 19th century) colonies mostly existed as sources of raw materials for industrialization at home, so killing off a massive source of cheap labor and replacing it with settlers would've be counter productive in the extreme. Asking about the Belgian Congo or French Indochina would probably be the best sources for a more in depth answer, while also illustrating that these colonial regimes were still very brutal.
This is all, of course, very generalized, but I hope it's useful to help you narrow down a future question that can give you a more comprehensive answer.