No, they didn't. Their ruling rested largely on how hostile the Colorado administrative agency acted in that particular case. They made no ruling on the larger questions, which is how they got Kagan and Breyer on board with the majority opinion.
That's not true. They ruled that the baker got a mulligan because government officials didn't show enough respect to his religious beliefs. It is still illegal and there's another case against him right now over this behavior.
No, it absolutely did not overturn protected status of LGBTQ. To quote Justice Kennedy, Colorado "can protect gay persons in acquiring products and services... the law must be applied in a manner that is neutral toward religion".