Racial, religious etc. discrimination harms society and vulnerable people. In small towns, isolated and rural areas, just one or two discriminatory businesses could keep a significant portion of the population from getting a job, shopping, getting a place to live etc. without leaving town. Even in a more urban environment, discrimination can force poor people to unnecessary waste time and money searching for a business that will accept their money in exchange for goods or services. Businesses have the ability to oppress people in their daily lives as much or more than government, especially in these days of a handful of mega-corporations, malls and big box retail dominating retail and services. Addressing government discrimination while allowing business discrimination requires tolerating discrimination and the hardship and oppression it will impose on unpopular minorities and society as a whole.
The business owner who doesn't like serving a customer because of their race, religion, gender etc is harmed much less when forced to serve that person than the would-be customer who has to find another place that will serve him/her is harmed. When a person can't get a job or a home because of race, religion, gender etc discrimination they suffer far more than the employer or landlord will suffer from being forced to treat that person as an equal. In addition, society as a whole is harmed by the impact of discrimination based on prejudice and hate.
Discrimination harms society by maintaining an impoverished underclass living with all the ill effects of poverty and oppression, effects which can impact everyone in the form of blight, large numbers of beggars, disease, crime, violence, rebellion and revenge.
Past experiences and the experiences of other places show us what happens when discrimination is allowed. Jim Crow laws existed during my lifetime and the negative effects from them still impacts life today. I don't believe that such discrimination will be as rare as claimed.