According to the establishment clause, the united states government is not allowed to national religion or favor a certain religion in anyway. This may give the impression that the Ten Commandments would not ne allowed in a government funded museum, however isn't exactly the case. As long as the museum only comments on the religions historical context and significance it is still constitutional. But because the museum is government funded, it would not be considered constitutional if they were to have prayer or host any type of religious events.
Separation of Church and state allows for religion and politics to not interfere with each other. In other words the government must maintain neutrality towards the idea of religion.
