Constitutionally, Religious Gatherings Must Enjoy the Same Rights as Protests

That's generally the constitutional test- if you are generally regulating things and not singling out religions, you're ok.

Now if a particular practice is essential to that religion, you may have to show a compelling government interest in order to force the religion to comply.

The problem, of course, is that if the government is explicitly or even implicitly allowing flouting of those rules then the compelling government interest is null and void. Fig leafs like indoors vs outdoors isn't going to cut it.

As a person who attends organized religious services several times a week, I can sort of see why the right to protest the Government may take precedence over anything else. It's the one right you really can't touch even in an emergency.

That being said, I really appreciated being able to attend a minyan last Shabbos (outdoors, with restrictions).

In reality though protests are hardly like any other outdoor gathering. Thousands of people are crowded together for hours and shouting (which projects saliva). Anyone can clearly see it is a hotspot for coronavirus transmission. Authorities are allowing (peaceful) protest though because of free speech rights. The same freedoms are not extended to arguably lower risk religious gatherings.

Santa Clara county, which has had daily protests, just allowed outdoor-only religious gatherings of 25 people or less last week. They also opened indoor shopping malls in the same order. They’re clearly not treating religious expression like the fundamental constitutional right that it is. It is easy to find similar examples all over the state. When the coronavirus situation stabilizes, the lawyers are going to have a field day.

The proper comparison is between law-abiding protesters and law-abiding churchgoers.

Yeah, protesters that break the law, especially by committing serious acts of violence or property damage, can expect to spend quite a while in jail. Many would say not nearly long enough.

For what it's worth if someone had sad - "Please have service outside." I think everyone who goes to church would have been happy. That wasn't presented as an option. Frankly to me the idea seems more like after the fact rationalization.