Well, if you live in a country with an official national religion, it should follow the teachings of that religion. If you lived in a 90%+ Christian country, it'd be fair not to open shops on Sunday. If it was a 90%+ Muslim country, it's fair not to open shops on Friday or not to sell alcohol/pork. If you live in a 90%+ atheist country, it's fair not to build churches and temples in public areas.
Those are pretty much how the majority wish to live, and the minority has to accept that. Or sadly, they'd have to get out. However, these days, there are very few countries that go that way. Even with a state religion, it's often like 70% of the populace, the others being atheists, agnostics, muslims, or christians. Secular governments are free to live without any religious influence whatsoever, but those where the public chose a religion will have to stick with one.
But... when you automatically assume that the same things are bad, then that's a problem. I don't care too much about homosexual marriage, unless there's significant financial benefits to getting married. It's a minor issue. But whipping for premarital sex, censorship, banning headscarves and prayer is a more serious matter.
Religion itself is a good thing. It's a form of philosophy, makes people think about the world, what lies beyond the universe, and gives people a meaning to their lives. Even if your religious belief is that there is no God(s), it makes you think about the bigger picture as a whole.
But moralism is evil. It tries to use religion as a way to get their political beliefs in. If someone doesn't like smoking, they claim it's against religion. Someone doesn't like smut or homosexuals.. fall back to religion.
Just about every religion spread through kindness, not by forcing their beliefs. The Islamic empires back during the Renaissance were the most religiously tolerant there, and crumbled shortly after they became more intolerant. They spread their beliefs far and wide by not forcing them. And part of the major support towards Atheism in modern society is in opposing the morality forced by religious institutions.