Because they weren't being violent about it at the time and because they were mostly focused on arguing or shaming people about their religion, aka Christians, and by and far went after white Christian, never Hispanic ones. The key here is that they can go after the people and no one would care because whatever, its not you or me.
The difference now, is openly attacking churches, which are a symbol of Christianity in itself. Doesn't matter who you are and what sect you're in, a church is a church and if they're willing to burn down one somewhere else, they're willing to burn down your local church. You can't ignore that, they're not arguing for you to forget about God, at that point they're willing to get of you for your faith.