This is a great question. It is probably a good idea to state the First Amendment first and then answer the question.
"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances."
There are two main points when it comes to religion. First, there is a separation of church and state. We can say that there are two separate spheres of influence. In light of this, the government does not have the right to encroach upon the beliefs of a person. A person's conscious should be allowed to be free to worship. In other words, we have a secular government that protects religion. This is different than other secular government, which might seek to suppress religion.
Second, the government should allow these rights not only for certain religions, but for all religions.