too many contradictions
for example, in genesis 'god flew over the water' but several days later, god created water
Whilst there is no proof/evidence that a God exists, there is also no proof/evidence that a God doesn't exist. Whilst previously we did explain many things through the God of the gaps theory, and now have a lot of scientific evidence to explain why things happen, this still doesn't disprove the possibility of a God. The idea of a designer having created the universe is certainly logical, as "nothing can come from nothing", it is simply many atheists look at an anthropomorphic God who lives in a cloud casting spells and close their mind to any other possibility of 'God', in which case of course it can seem illogical.
Whilst atheists can provide evidence against religions and how they are flawed, they cannot provide evidence as to a 'God' being inexistant. The problem I think is because many have this exclusive, fixated idea of a God, and don't open their minds to any other possible forms of this designer. As I said before, you can try and disprove a religious belief of God, but you cannot disprove God itself - if we were created by a God, he doesn't necessarily have to be omnipotent, or omnscient, or benevolent. He doesn't have to be one God, he could be a team of 'Gods' who worked together in creating the universe. People can't limit their understanding of a designer as being either option a) the christian one, option b) the islamic one, etc etc.