Fake. Well, the first two sentences are fake but the second part ("Millions of innocent men..."), is legitimate and comes from Jefferson's Notes on the State of Virginia, Query XVII. http://www.monticello.org/site/jefferson/superstition-christianity-quotation
Politics, Religion, Separation of Church and State, Forcing Religion on Others, Religious Freedom, Freedom of Religion, Freedom from Religion, Thomas Jefferson, America, United States, United States of America, USA. Erecting the wall of separation between church and state is absolutely essential in a free society.
Rule of 3~ Life, liberty, and happiness might very well be the three most important words in American history. Why did Jefferson choose three rights instead of, say, twelve? Jefferson was a skilled writer and his famous phrase reflects a rhetorical technique that can be traced to ancient Greece—a figure of speech using three words to express one idea.
Click through to Monticello site and the actual reference. It comes from Jefferson's Notes on the State of Virginia, Query XVII. The material that actually precedes the quote is: "Difference of opinion is advantageous in religion. The several sects perform the office of a Censor morum over each other. Is uniformity attainable? Millions of innocent..." etc.