There is a huge difference between religion being the basis of the community and race. When it's religion then people have the option to convert. When it's culture, people have the option to convert. When it's race there is no option for the excluded races to ever be accepted.
So basically, the faction of the alt-right which is racist is seeking to exclude all human beings who aren't born into the right race. There is no compromise, no surrender, you either are born into that identity or you're not. You get no choice to join, or integrate, or belong.
As far as religion goes, if the churches aren't segregated then maybe it's not racist. But I don't have enough information on that to determine. Of course racial bigotry isn't the only kind of bigotry that can exist but the racial kind of bigotry divides people of the same ethnicity, with in some cases the same ancestors, over a concept which doesn't really have any basis in science.
For example, Malcolm X was killed and he had white ancestors. But because America was obsessed with race, he was categorized as black, and took on a black identity. In other examples, you can have black and white Americans who share Native American ancestors. They might have more in common genetically with each other than African immigrants or European immigrants. Race divides them both against each other even if they are the same culture and ethnicity.
And then the concept of race also distorts medicine. Race based medicine vs personalized medicine, which is better? Personalized medicine is always going to be more accurate than race based medicine.