Hatred for Native Americans was far from universal, although it was more common in the United States than in Canada. Certainly derision and paternalistic attitudes were very common, and often the contemporary critiques of treatment towards the aboriginal populations was directed more at the methods, not necessarily the aims. In this sense, I mean that it was up until relatively recently in most places in North America that the mission towards the aboriginals was a 'civilizing one'.

The United States has a particular history with Natives that was largely developed in the late 18th and early 20th century through heavy military conflicts in which the aboriginals were involved. It was to the British military's benefit to portray the aboriginals as evil and terrifying, first to justify their protection over the colonies, and then as a military propaganda tool as those tribes became allied to the British causes. This created a mindset in the American psyche that lasted throughout much of the 19th century of the dangerous aboriginal; this fear was so acute that during the War of 1812, William Hull surrendered the entire fort of Detroit without a shot fired, such was his fear of what the aboriginals could and would do to him and his men. These fears, so effectively created, would have a great impact as the United States pushed west in the coming half century.

However, even this carefully cultivated hatred had its limits. Take for example the Sand Creek Massacre of 1864, which involved the slaughter of an unarmed settlement, largely women and children. It was too much of a slaughter to justify. On the other hand, while a conciliatory treaty was signed shortly afterwards, largely driven by guilt over those actions, said treaty was basically ignored. So, as was often the case during the 19th century in the United States, expediency and expansion trumped the public moral character that the country claimed to possess.

Contrary to what is commonly believed, from the very beginning of the enslavement and extermination of the original peoples of the Americas there were people who thought this was absolutely morally unacceptable and attempted to fight it. Many earnest priests were opposed to this absolutely abhorrent treatment of fellow human beings (even if their superiors de facto weren't). Unfortunately I don't have access to my personal library at right now (although I will provide sources when I do) but this wikipedia article shows one example. I am sure someone with more expertise in the area of slavery in the Americas can easily provide many, many examples.