I think in order to answer this question you have to ask how each phrase is used today, and how was it used in the Constitution. The First Amendment to the Constitution says"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."
This has been taken to mean that, in the words of Thomas Jefferson, there is a “wall of separation between Church and State.” Undoubtedly Jefferson meant that no CHURCH or denomination should control the state, but he did not mean that no religious convictions should guide leaders in the exercise of their state powers. Freedom of religion meant that congress could not establish a state religion, or prevent people from worshiping according to the dictates of their own conscience. The people were to be protected from state intrusions into their religion.
“Freedom from religion” is used today by many people to restrict the exercise of religion in the people. That the freedom to tell your neighbors about your beliefs must come second to the desire of some not to hear what you believe. The Freedom From Religion Foundation (FFRF), for example, is primarily an atheist organization wishing to revoke the use of chaplains, end Bible instruction in public schools, disestablish a National Day of Prayer, end faith-based prison programs, and stop “spirituality” in health care by the Department of Veteran Affairs.
The FFRF supports billboards saying “the God of the Old Testament is arguably the most unpleasant character in all fiction,” “I don’t believe in God, because I don’t believe in Mother Goose,” As my ancestors are free from slavery, I am free from the slavery of religion,” “Faith is believing what you know ain’t so,” There’s probably no God, so quite worrying and enjoy your life,” “The Bible: A Grim Fairy Tale,” “Imagine No Religion,” “Praise Darwin: Evolve Beyond Belief,” “Keep Religion OUT of Politics,”
The goal of the “freedom from religion” crowd seems to be to marginalize those with religious beliefs, to characterize them as extreme right-wing bigots, and to not let their voices be heard in political discussions. The thought is to box religion up so tight that all decisions of right and wrong, what is best for the country, and what our national priorities and values are must be expressed in purely secular phrases.
Those who believe in freedom of religion believe as Ronald Reagan did that “Freedom prospers when religion is vibrant and the rule of law under God is acknowledged.” Or, as President Bill Clinton stated, “Sometimes I think the environment in which we operate is entirely too secular. The fact that we have freedom of religion doesn’t mean we need to try to have freedom from religion.”
So, today, in an important sense, freedom of religion is the opposite of freedom from religion.