"Homo fuge" is simply the Latin for "Fly, man!" These words appear on Faustus's arm after he makes his diabolical pact with the Devil, selling his soul in return for twenty-four years of incredible power. The words refer to a verse in the Bible, 1 Timothy 6:11.
But thou, O man of God, flee these things; and follow after righteousness, godliness, faith, love, patience, meekness. (KJV)
Here, St. Paul urges Timothy to fight the good fight, to turn aside from the things of this world to focus on what really matters to a Christian. The above passage comes right after Paul's famous warning that love of money is the root of all evil.
It's ironic indeed that the words "Homo fuge" should appear on Faustus's arm at this point. Instead of fleeing the world and flying towards God's righteousness, God's love, this man—Faustus—is actually about to go in the opposite direction; to embark upon a life of earthly power and wealth. In any case, Faustus is trapped; having made his bargain with Lucifer, he cannot flee to God, for he's certain that the Almighty will cast him straight down to hell.