This is written primarily as a response to the very pejoratively titled "Crazy Atheist Faith!" by the equally pejoratively named "Charles Dumbwin".
Let's start with the most obvious gap in reasoning – if one could call it reasoning in the first place – that of Atheism being a religion. You'll find that what all religions share is an adherence to the belief that the "supernatural" is a real and tangible thing. Be it in the form of snakes talking (vocal chords much?) to the idea that gods can walk the earth in ever-changing Avatars.
Where is this supernatural set of beliefs to be found among the atheist masses? Adherence to the idea that science explains – or can explain – all we observe is built around the very key idea that all things which exist are natural. That is they are natural because they are real. Nowhere in atheism will you find the ingrained belief in supernatural agencies of any kind.
This brings us swiftly around to the other fallacy apparent in the article – Faith, or the obvious lack thereof. As the author so eloquently states – faith is belief in something without evidence. Rather easy to see why this silly assertion that atheists are faithful is very much false, or at the least a gross oversimplification of how complex trying to understand this world really is.
We as atheists do not believe the "To believe that this wonderfully complex and beautiful Universe just simply created itself " due to some unfounded faith. It is the simplest answer to the question, if we bring any of the hundreds of gods into it we're just creating more questions and no new answers for them. Which is more likely – A complex universe arises by itself, or a god complex enough to build said universe arises by itself? God just extends the question of where it all began backward by one step.
As for the "theory" of evolution – are you familiar with the concept of semantics? Words can mean more than one thing, as is the case for theory. Theory in the scientific sense is an idea that has been built up and tested to try and explain the observable universe around us. Does it come as a shock that gravity and germs are also "just" theories?
Next I'll be hearing that HIV causing AIDS is also just a silly theory.
No my dear Charles, it's not faith to say that an apple and a feather fall at the same velocity in a vacuum, it is trust. Trust in the fact that the universe can't just change its laws at a whim, it is trust in the fact that 1 + 1 = 2 today, it will be equal to two tomorrow too.
So don't have faith in science my fellow atheists, rather TRUST in science.