The European's were racist in their dealings with both the Native Americans and the Africans. The word racism is often too harsh of a word for some, and they want to find other reasons that one's behavior exists. But the white Europeans saw one major difference in them and the strangers of North America and Africa and that was skin color.
But I also think it is very important to look at the aspects of religion and economics. Religion was probably as important as their racist views toward the natives and africans. The teachings of Christian leaders fueled much of the activity of that time period. The Europeans felt justified in their actions of murder and destruction because they were intending on teaching the "savages" the peaceful religion of Christianity.
And finally economics was the third factor. The natives stood between the Europeans and large amounts of land and resources. The africans were also available as slaves and large profits in the plantations of the new world.
The Europeans saw a difference in skin color and used religiona and ecomonic justification in the harsh treatment of natives and africans.
It is not that racism was used to separate Europeans from native Americans and Africans. Rather the practices like this separation was part of racism.
The cause of racism, is primarily racial prejudices. People who are in power and prosperous, tend to look down upon others who are not that well off.
In the initial stages of migration of Europeans to the American continent they found it to their advantage to, fight and defeat the local Americans, to take away fro them their lands, and to keep them weak and ignorant. To justify such actions they had to convince themselves that they are superior to them. This feeling continued even when there were no such economic compulsions.
Similar things happened in case of Africans because of the economic benefits of enslaving them.