Yes, it should. Why should I have less rights and why should the religious have more privileges than me just because they believe in a god? Too many Christians and overall religious people are forceful and bigoted and try to make everything about their religion and their irrational faith and belief system. If I want to be an atheist, why should they have the right to stop me?
The establishment clause should apply equally to both religious and atheists. It should not matter what you believe in personally when you are in business with different customers. I believe that personal religion has no place in the place of a business. That should be considered outside of the business.
Religious people as well as atheists should abide by the establishment clause. Whether professing your own specific ideals of God or a lack thereof, there should always be a separation of church and state. Atheists should be allowed to believe in no God at all just as freely as Religious people believe there is a God.
Yes, the establishment clause should apply equally to both religions and to atheism, because too many atheists who try to get rid of all references to God try to replace it with the government saying that there is no religion at all. If I want to pray at school, why should they have a right to stop me?
The establishment clause only states that the government can't find favor with a religion and they can set a preferred religion or a state religion. The separate religions aren't particularly protected and it doesn't do much to say anything about an individual being religious or a individual being an atheists. Its a law that applies more to the government rather than the entities it seeks to protect.