My question is, that how could it be possible for Marlowe to deny the existence of God while at the same time, produce such a masterpiece like Dr. Faustus whose topics are God, Lucifer, angels, virtue and sin, Heaven and hell and most of all, the conclusion itself. If this is the work of Marlowe, then why is he called an atheist?
TLDR: 1 - Marlow was not an atheist in the modern sense. 2- Dr Faustus is not as clearly religious as it first appears
Let's start by pointing out that "atheism" doesn't necessarily stop an author from writing about theism. Umberto Eco, for example, is a professed atheist yet is the author of The Name of the Rose, a novel set in a medieval monastery which examines many themes in religion and belief. There is no particular problem, therefore, in reconciling the religious elements in Dr. Faustus with having been written by an atheist.
That said, the question of Marlowe's atheism is not a straightforward one. Not least because the definition of "atheism" used in the Elizabethan era is not the same as the one used today.
Elizabeth's father, Henry VIII had founded the church of England and made himself the head of that church. Therefore, to be an atheist in England was literally equivalent to treason: in denying God, you are denying the monarch's divine right to rule. By Elizabeth's time, this was even more problematic because her succession to the throne was dependent on the legality of Henry's divorce from Katherine of Aragon, which he was only able to push through as the head of his own church. So, by the time of Marlowe, the term "atheist" had acquired a wider subtext equivalent to "anarchist" in modern usage.
For example, Marlowe is often counted among the "School of Night", a loose group of critical thinkers including Sir Walter Raleigh. These men were often referred to as atheists in their era but a modern examination of their writing and behaviour suggests they are more what we would today call religious dissenters or perhaps agnostics. People who doubted the literal truth of the Bible and its interpretation and practices as laid down by the Church of England not, necessarily, people who denied the existence of God outright.
Take Raleigh as an example. In his book "The History of the World" he wrote:
For the rest; I do also account it not the meanest, but an impiety monstrous, to confound God and Nature; be it but in terms. .... It is God that commandeth all: it is Nature that is obedient to all: it is God that doth good unto all, knowing and loving the good He doth: It is Nature, that secondarily doth also good, but it neither knoweth nor loveth the good it doth.
In other words, God is good and lord over all nature. Does that sound like the writing of someone who rejects the existence of God? Raleigh was also known as an aider and supporter of puritan priests. Rather, Raleigh was someone who saw the value of rational thinking and was prepared to use that thinking to challenge the orthodox dogma of the church and - by extension - the state.
So, having established that "atheism" in the 16th century had a much wider meaning than it does today, let's return to Marlowe. Much of the evidence we have of his atheism rests on the charge of a single informer, Richard Baines. Baines was a spy, whose work was to ferret out Catholic sympathisers in protestant England. His continued employment was, to some extent, thus dependent on him finding such sympathisers. He is the only direct source we have for Marlowe's atheism which, in itself, seems a valid reason to question whether Marlowe was, in fact, an atheist.
If we presume that Baines was telling the truth, here are some of the things he claims Marlowe to have written:
Christ was a bastard and his mother dishonest
the woman of Samaria and her sister were whores and that Christ knew them dishonestly
St John the Evangelist was bedfellow to Christ and leaned always in his bosom ... that he used him as the sinners of Sodom
Looking at these statements in the light of how Elizabethans defined "atheism" it seems likely, then, that Marlowe was an "atheist" in the same way Raleigh was: someone who doubted the literal truth of scripture rather than doubted God outright. Nothing in these statements or any of the other 14 items Baines laid against Marlowe suggests an absolute rejection of God.
In fact, if we look at Dr. Faustus, it is arguable that the play itself is espousing this kind of "atheism", which rejects dogma but not Christianity as a whole. The ending of the play falls in with the dominant Christian concept of heaven and hell, suggesting a broad acceptance of scripture. But as for the details, take the following lines from the play:
Within this circle is Jehovah’s name/ Forward and backward anagrammatized;/ The abbreviated names of holy saints.
How! Bell, book, and candle, book and bell, / Anon you shall hear a hog grunt, a calf bleat, and an ass bray, / Because it is St. Peter’s holy day
In both these cases, Faustus can be seen as critiquing organised religion. In the first instance, he is subverting the value placed on the holy name of Jehovah. In the second he is comparing the liturgies of religious rituals with animal noises.
Later in the play, the Pope's men urge God to curse Faustus for his behaviour, chanting in Latin. But nothing happens. This pokes fun at the idea that God can be invoked through religious ritual. It can also, of course, be read as suggesting that God does not exist. By the end of the play, all we can be certain of, in a religious sense, is that the devil exists. In which case we could argue that the play is, in fact, wholly atheist: rejecting God and using Satan merely as a plot device.
Boas, Frederick Samuel (1940). Christopher Marlowe: a biographical and critical study. Oxford: Clarendon Press.
Kocher, Paul H. (1940). Marlowe's Atheist Lecture. The Journal of English and Germanic Philology.
Webb, Susanne S (1969). Raleigh, Hariot, and Atheism in Elizabethan and Early Stuart England. Albion: A Quarterly Journal Concerned with British Studies.