I am indeed religious and I, personally do not feel prosecuted at all. Quite the opposite. And I agree with you that First Amendment served religion well.
I am very happy to see religion divested of state power. Power can only corrupt any religion. Does atheism have state power yet? No. At least, not in an active way. But, as state power and influence grows, this power squeezes religion out of the areas where it used to be permitted. State used to be not involved in education, social security, medical services. Now that it's there (and it's a good thing it's there, don't get me wrong), religion has been pushed out.
So far, it has all been in moderation. I can still send my kids to religious schools, or ask my community for help with medical bills. But, if certain forces have their way, I can see religious education abolished as harmful to children. I can see "single payer" medical system that will make privately (iow, religiously) funded medical help unavailable. And so on. This is so far back in the future, I can't see it clearly from here. I am comfortable with where we are now, and a bit more of state-church separation may actually be healthy (such as removal of the word "marriage" from the law of the land). But, if the trend continues, it _may_ lead too far.