I think a 'thing' against anyone is usually, though not always, based on some reasoning and some emotion - the emotional response of moral convictions is a response to certain facts. So despite the women at a Muslim wedding consenting to covering their heads or wanting segregation, it might just feel wrong and against moral principles that are very important to the business owner. I think the 'thing' they have against Muslims would be based on thinking and perceptions, which people are not always able to articulate.
This bill seems to me to be about how much freedom to allow the business owner - given that a job takes up a large part of your day and thought process and in the case of a business owner, takes up a large part of your life and can be like your child and often takes precedence over your actual children, I can understand giving business owners some freedom.
I think market forces may lead to many business owners being practical and setting aside their deeply held moral convictions in the interests of profit. And not just in this scenario.