Sure, but it's also widely understood that the vast majority was due to disease-- which would have spread simply due to contact of any sort. The only way to prevent it would be to quarantine the New World, and that's not even vaguely realistic. Bottom line: while the Spaniards no doubt did bad things, that massive death toll stems from something that wasn't specifically or uniquely their doing. If the disease problem hadn't existed, then the death toll would be very small compared to what we see in OTL. In fact, when we look at the number of Native Americans in Latin America, and the degree of mixing of population, and then contrast that with the situation in Anglo-America... well. The impression arises that the Anglos were far, far more thorough in any active extermination efforts. And that the Spanish primarily get the bad rep as "ultra-exterminators" because they were the first guys "on the scene", and thus doing their colonising when the waves of disease burned through the New World.
Naturally, this does not excuse any atrocities that were committed, but it does indicate that the image of Spanish colonialism being uniquely worse than that of other countries is not correct. (And in fact, Spanish colonialism may in certain ways have been marginally "less bad" for Native Americans than Anglo colonialism.)
OTOH, the Spanish colonised the most densely populated Native lands. US and Canada had only a fraction of the population density of Mesoamerica to begin with. That said, yes, the Anglo (and, in some phases, Portuguese; different densities also being a factor in Brazil vs. Spanish Andean and Central America) settler colonialism tended to want to
remove the Natives, while the Spanish largely extractive colonialism tended to be content with
brutally exploiting them. Remarkably in Argentina, Uruguay and, to an extent, Chile, all colonised by Spain, the pattern is closer to US/Canada/Brazil than it is to Mexico/Peru/Bolivia. And you don't really find so much people with any traceable Native ancestry in modern Cuba, forget about recognizable Native groups there at all (unlike pretty much everywhere in the mainland, US, Canada, Argentina and Brazil included, main exception I know of being Uruguay).
To elaborate a bit, the point is only secondarily the colonizing nation involved, though of course Spain, Portugal, England/Britain and France had their specific strategies, constraints and preferences; its more the nexus between the native settlement pattern and the colonial
local option for exploiting the land (in turn conditioned by political and cultural choices in the metropolis and in the colony, ecological and economical situations, sociopolitical bases of the colonization itself, etc.) the defined how badly the natives would have fared, usually on a scale from
badly to
horrifically worse anyway.