As an atheist should all my beliefs be protected under the first amendment since the supreme Court recognizes atheism as a religion for practical purposes. And if so, are all beliefs protected regardless of the stem from religion, science, or anywhere?
Should all beliefs be protected like religious beliefs?
This is a situation where Freedom of Speech, and Separation of Church and State tend to collide. If government is desired to be impartial, then yes, any public institution, be it courthouse or school, shouldn't be about religion. A school should be able to offer a bible studies class if the community desires it, as well as equivalent options for Islam, Judaism, and whatever else. It should be an OPTION, not an educational requirement, however.
I'm purely speaking on government though, a private business SHOULD have the ability to say "we won't serve you here". If a restaurant in Memphis can legally post a sign saying "No blacks allowed". Let them. Why would you want to spend your money there regardless of your skin color? It's their decision to post that sign, and accept the consequences that come with it.
I wouldn't claim racism if a black church said I can't be there because I'm translucent. I'd take my shiny ass to another church that better represented my religious values. Forced acceptance in the name of legal protection can cause just as much discontent as forced segregation. If a group or community wants to self-segregate, let them!
Why force people to be where they're not wanted? We're now seeing the pendulum start to swing back from Jim crow era to "minority privilege". All men may be created equal, but not all are born into the same situation with the same skills and abilities. That's not oppression, it's cold reality. I feel that humans should focus more on making the best of the hand they're given than demanding the govt give them a stepstool because they were born shorter than average.
So in a sense, yes and no. Atheism is not the same as "science as religion" though some would treat it that way. It's like free speech, once you start adding conditions and exceptions to the rule, it isn't free speech anymore.