Religions often run in families and have very strong sticking power, in a way that's different from a college student turning to nihilism. For many people, their religion is not very changeable because it's a major part of their identity and without it they would not be properly themselves and don't know what to do and it would cause them great alarm.
Religions are often very sticky by location or by cultural subset, so if you decide to discriminate against religions, often you're not really discriminating against someone's free thought, but just where they happened to be born and what kind of culture they grew up with.
> at least in a free society
Lots of religious people do not come from societies one would reasonably call "free".
The things you've said certainly make sense but I feel like much of that also applies to political ideology. It certainly seems to me like much of that ideology is at least partly subject to location and culture. In particular I feel that a large part of our individual ideologies are based on our past experiences and the way those experiences shape our perspective of the world at large.
Edit: If we're going to use the logic that religious views should be protected due to their inherent "stickiness" relating to family and culture, and other aspects out of one's immediate control, I'm not convinced that other ideological views are any less "sticky" and thus not equally worthy of protection.
The specific question that prompted this was, why don't we protect Nazism the way we protect religion, and to that I'd say that I have heard of exceedingly few Nazis who have inherited it from their parents and feel the need to keep up external trappings of Nazism for the sake of family or social status. (The only example I can really think of is the Gaede twins, who renounced their mother's ideology by the time they were adults, and if you refined the question to not discriminating against minor children professing Nazi beliefs at their mother's direction, I am totally fine with figuring out a way to write a non-discrimination law about that.)
I don't really find that ideology is anywhere near as sticky, as I've had a much easier time discussing nuances with ideologues compared to religious people, and, more importantly, ideology is just nowhere near as stand out.
You can be a communist without anyone knowing. I have a set of some very odd beliefs, nobody really knows unless they ask.
You can't quite do that with religion when you have days you can't eat meat or you can't work because you have to go to a special building or what not. Or often religion instructs you to talk about it. Ideology can stay in your head; religions (properly followed) tend to be disruptive to one's entire lifestyle, so if a society doesn't protect it, it can as well declare the religion invalid for what that's going to do to it.
Which might be what the society wants to do, but you should understand what it is that you're doing.
Religions are often very sticky by location or by cultural subset, so if you decide to discriminate against religions, often you're not really discriminating against someone's free thought, but just where they happened to be born and what kind of culture they grew up with.
> at least in a free society
Lots of religious people do not come from societies one would reasonably call "free".