Our founders wanted freedom to have religion or freedom to NOT have religion. They were running from religious tyrants, so you are wrong. Our constitution guarantees people of the United States the right to pursue happiness! If getting married makes gay people happy, then you don't have the right to deny them their happiness, tyrant!
No, you're wrong there. In the time of our founding there simply was no atheist movement, certainly not within our government.
When the founders spoke of freedom of religion, they were thinking of a situation like the Church of England specifically, where one branch of Christianity was enforced by the government. It's a complete misnomer to state that our country wasn't founded ON religion though, I mean our Declaration of Independence speaks of God. Our Congress has a clergyman, and opens EVERY session with prayer. Our national monuments are packed full of religious symbols.
In their time, an atheist was unthinkable. Remember, they thought the indians were savages because they didn't believe in the monotheistic God.
The freedom of religion has totally been misshapen by those with agendas. Heck, I'll go even further, at the time they signed the COTUS many of the colonies/soon to be states DID have official religions, and that is the way the founders intended. Each state could have religion as they chose, free from the FEDERAL government intervening. If one state had a religion you didn't like, you simply moved to another.