The short answer to this question is yes. The most obvious parallel is that both the historical Faust and Christopher Marlowe were men about whom legends began to circulate soon after their deaths. In Faust's case, rumors spread regarding sorcery and a pact he had made with the devil, handing over his soul in exchange for "secret" knowledge and magical powers. The stories about Marlowe did not, for the most part, involve the supernatural, but some of them touched on religion and the allegation Marlowe was a "blasphemer" or an atheist. Present-day researchers seem to believe Marlowe was probably involved in espionage in the service of the Queen. His death at the age of 29 in a tavern brawl has generated endless speculation. In the nineteenth-century, when romantic myths were often invented about great men of the past, it was asserted that Marlowe was killed in a fight over a prostitute. In the typically euphemistic language of the period it was stated that he was knifed to death in a quarrel over "bought kisses." Though most historians now believe the dispute concerned something as mundane as paying the tavern bill, it's entirely possible that if Marlowe was involved in covert government work; he might have been killed by foreign agents or eliminated by others in the Queen's service for reasons we'll never know.
Apart from rumors and speculation, there is a deeper reason he was similar not necessarily to the historical Faust, but to the literary personage Marlowe created. In Marlowe's tragedy, Faust is dissatisfied with his life and is seeking something higher, something spectacular that will set him apart from other men. It's not enough for him to be a scholar, an ordinary person. He wants magical power and knowledge. He doesn't simply want women—he wants the most beautiful woman in history, Helen of Troy. Marlowe himself evidently wasn't satisfied either with the careers his university education would have opened to him or with his work as a writer. Even if he wasn't actually a secret agent, he had a reputation as a brawler, as a man living much of his life outside the law. In this sense he resembles his creation, Faustus.