Looking back at history you had lots of events where people were killed over religion, like the 30 years war. Why was it such a big deal what creed ones neighbor followed? Why was it necessary to burn heretics? I'm probably showing my post-enlightenment thinking here but it's such an alien concept to me.
You're exactly right when you say post-Enlightenment thinking; one of the biggest contributions of the Enlightenment to western society was its emphasis on a universal human nature, an idea that was (in my opinion) a reaction to the very wars of religion you mention.
What is interesting to note is that under the Roman Empire, although all religions were permitted technically, Roman citizens were still expected to sacrifice on behalf of the emperor and to acknowledge his sovereignty over them. This is in large part due to the idea that the church (i.e. Religion) is NOT separate from the state but is in fact mandated by the state. This policy continues throughout Late Antiquity and into the medieval period. You can see in Theodosius making Christianity the official religion of the Roman Empire. You can see it in the Admonition Generalis of Charlemagne (789 AD). And you see it with the Peace of Augsburg's "cuius regio, eius religio," which granted each prince of the Holy Roma Empire the ability to institute their own religion (Lutheran or Catholic) in their own state. These were not just state approved religions, but state promoted.
For more information on this topic, I recommend Abigail Firey's The Contrite Heart. It's about how Carolingian secular law blends with ecclestiastical law and has a great analysis of how religion was an official extension of the state.