This is perhaps one of Neitzsche's best works. It is filled with many beautiful aphorisms and deep insights into human psyschology and the nature of religion and philosophy that anyone, irregardless of thier own world-view, can appreciate. Yet despite these strengths, there are also weaknesses.
_The Gay Science_ is wherein enters Nietzshce's famous phrase that "God is dead". Although Nietzsche has acquired much fame for this infamous slogan, his actual arguments against the existence of God, in my opinion are weak.
I concede with R.J. Hollingdale, who rightly points out that the German philosopher "tended not to offer a systematic exposition of his views in a single place". This must be kept in mind because its very easy to find "flaws" in many of Nietzsche's assertions simply because the arguments for his position don't always precede his position. Often, the reader will be surprised to find substantiation for a view in another chapter of the same book or even in another book! This naturally forces one to be a bit cautious before hastily criticising Nietzsche.
Taking into consideration this precaution, I still think there are certain flaws which in regard to his critque of the "God concept" appear to stand out. First of all, Nietzsche acknowledges that even though none of the proofs for the existence of God have stood the test of time, there haven't been put forward any irrefutable proofs against God's existence. He is aware that on the level of tight logical reasoning, (on the level of proofs and counter-proofs), the existence or non-existence of God cannot be logically settled. To settle the issue, to "make a clean sweep", Nietzsche finds what he considers to be the psychological and historical reasons that led to the creation of the God-concept. Having ascertained the "reasons" for which humans came up with the God-hypothesis, he is of the opinion that the matter is closed. The problem with this approach is that i) if it is acknowledged that God's existence cannot be logically proved or disproved, then at best it should lead one to agnosticism, and ii) simply because one has come up with explanations of how God could have arisen still isn't a definitive reason that He doesn't exist. All Nietzshce has done is exposed possible motives that led to the "creation" of God, but such a stance doesn't render God's non-existence decisive. Yet Nietzshce refers to the "stupendous concept, 'God'" also calling Him our "most enduring lie" (GS 344). For such strong statements one would expect strong reasons, yet exposing the human-all-too-human reasons for creating God makes the non-existence of the God tenable at best, but certainly not decisive.
Furthermore, Nietzshce's claim that God is a fiction because he is the product of human-all-too-human "need" can actually be turned against him. What if these needs actually exist within humans too point them towards God? That humans are painfully aware of their own ontological finitude is attested to by scores of literature and poetry written over the ages. Yet what if the awareness of this incompleteness which humans sense within themselves, and which leads them to desire a Beyond, is actually a type of "homing-device" directing them to what really exists above. Hunger leads us to food. Thirst to water. Why can't the pain of our finitude lead us to God? When an infant is removed from his mother, he becomes painfully aware that "something is missing". Until the child returns to his mother, he will remain uneasy and perhaps even cry. Can't the human misery that stems from our separateness and isolation be a signal that just as we desire our physical mother in the world, so too do we desire our Spiritual Mother in the Beyond? Once deprived of the beyond, humans begin to worship substitute gods. One merely has to look at the ideals worshipped over the last 200 years: freedom, democracy, liberty, communism, nationalism, etc. Humans are beyond doubt worshipping animals. But why? Could in not because of our desire for the Divine? Of course, this is not a "decisive proof" for theism any more than Nietzsche's differing perspective is for atheism. But it must be kept in mind that it is just that -- a perspective. Ironically, Nietzsche argues for perspectivism, yet his perspective is supposed to be truer than that of those who believe otherwise!
Although Nietzsche does give "reasons" for his atheism, for him his rejection of God is ultimately a priori. He doesn't disbelieve because no proofs are available but its a principle from which he starts. He writes "Our presuppositions: no God" (WP 595). He makes an even more definitive statement corroborating this view in his autobiography, Ecce Homo: "God","immortality of the soul," "redemption", "beyond" -- without exception, concepts to which I never devoted any attention, or time; not even as a child. Perhaps I have never been childlike enough for them? I do not know by any means know atheism as a result; even less as an event: it is a matter of course with me, from instinct (2:1). Keeping these words in mind, it is worth comparing them to what Walter Kaufmann writes of Nietzshce's views about philosophical systems: "The thinker who believes in the ultimate truth of his system without questioning its presuppositions, appears more stupid than he is; he refuses to think beyond a certain point; and this is according to Nietzsche a subtle moral corruption" (Nietzsche 81). And yet despite all of Nietzsche's diatribes against those who lack an intellectual conscience, he appears himself to be guilty it when it comes to God. He is thinks that his genealogical-subversion of God "wipes the slate clean". But his slate was empty from the beginning!