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Oye.
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I going to try to say this simply.
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Religious Freedom is guaranteed by the Constitution, just like Freedom of Speech. But that does't mean they are consequence free.
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For example, if I write (which is a form of Free Speech in this country) that I think Hillary Clinton is a terrible person, a traitor to liberal causes and a not a very good feminist, I am free to say that. If I then apply for a job on Hillary Clinton's campaign staff and they respond that I am not the right fit - because of my statements - that is legal. I am free to say that Hillary Clinton sucks - and they are free to use those statements as part of their evaluation of me.
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Just like the Christian brothers Benham brothers were free to say "homosexuality and its agenda are attacking the nation" and "demonic ideologies" are taking hold in colleges and universities. The Home and Garden TV network is free to say, we aren't giving you a TV show because a large percentage of our audience is homosexual. (LINK - to this old topic)
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Free speech protects your right to say things, it does not protect you from repercussions.
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Freedom of Religion has similar, but more limited repercussions. Fro example, you can't be terminated or have your hiring effected by your Religious beliefs (obviously there are exceptions for Religious institutions).
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Which brings us to the kurfufle de jour. Atlanta Fire Chief Kelvin Cochran.
.Chief Cochran wrote, and self-published, a book about his religion. Of the 160 pages, 80 of them were devoted to explaining why gays were perverted and going to hell (from a supportive article LINK).
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This book being published did not get him into trouble, despite what might have heard or read (even in the LINK I gave you).
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No, what got Chief Cochran into trouble was that after writing it, he distributed this book to his subordinates in the Fire Department. When the boss gives you a book that calls out your subordinates as sexual perverse sinners, people deserve to burn in hell and should be shunned in life, well that is out of bounds as a manager.
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Had he distributed that same self-published book stating (also based on the Bible) that female Fire Fighters should burn in hell if they worked during the menstrual cycle - he would have been fired.
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Fire Chief Cochran's Freedom of Religion allows him to believe and say whatever he wants. But once you say things, it is no longer consequence free. And if you are a public employee and a manager where anti-discrimination laws apply, they your actions in public and on the public payroll must meet certain standards.
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Fire Chief Cochran is allowed to hate and disapprove of whomever he pleases - after all hate seems to be a big part of his life (1/2 of his self-published book is dwells, rather obsessively with the perversions of gays) - but as a manager he isn't allowed to bring that to work. Nor is he allowed to actively push that hatred on to his subordinates in a discrimination free environment.
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You want to hate fags, go work at Hobby Lobby.