I don't doubt that there are people who operate on a "well, I am a Muslim so I want Muslim employees" scheme or similar ones (woman, black, young), but I do believe that this should be covered by freedom of association.
I do understand that you think otherwise, I have met many people who see things differently.
There is nothing to "misunderstand" here, this is not algebra but law, and law often erects artificial and arbitrary barriers in the middle of things, in order to further some specific interests or agenda.
The closest analogy I can find is the concept that commercial speech deserves less protection than private speech.
It is a matter of opinion and prevailing mores. In my opinion, becoming an employee is a voluntary decision (unlike, say, being drafted into a war), and should be treated the same as becoming a trade union member or a volunteer in a church organization.
I do understand that you think otherwise, I have met many people who see things differently.