There are two reasons that design is ruled out almost a priori.
Well, I applaud you for admitting that atheists sometimes rule out God a priori. I don't think many other atheists on this thread would admit that. I believe that with many atheists, it's really not "a lack of belief", but rather a committed belief in atheism. They're committed to the belief that God does not exist and move forward on that basis. So thanks for being honest about that. You know, it used to be the accepted idea that the universe has always existed, but then the Big Bang came along and messed that up. So atheists began making up all sorts of alternate models for the universe to avoid a beginning. Recently, some of them have been conceding that the universe had a beginning...basically saying to the rest "Hey, the universe had a beginning. Deal with it." Now we have the fine tuning which is messing things up for the atheists also and some of them are willing to deal with it, but they come up with alternate explanations for that also. If you look at the link I supplied before, you will see several scientists concurring that the universe is fine-tuned. Atheists have been accusing believers of offering a god of the gaps argument for years, but haven't some scientists been doing that --coming up with scientific explanations that seem far out only because of a commitment to atheism? Anyway, Professor Richard Lewontin, a geneticist, seemed to think so. Read what he said about that:
‘Our
willingness to accept
scientific claims that are
against common sense is the key to an understanding of the real struggle between science and the supernatural.
We take the side of science in spite of the patent absurdity of some of its constructs,
in spite of its failure to fulfill many of its extravagant promises of health and life,
in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment,
a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that
we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations,
no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for
we cannot allow a Divine Foot in the door.
http://creation.com/amazing-admission-lewontin-quote
However, I think you are a little confused about what Christians say about God and how he relates to his creation...
First, what good would it do for scientific progress if we just assumed God did it? We would be done exploring and figuring things out.
Christians are not against scientific advancement. Heck, the scientific endeavor
began with the motive to understand how things worked in God's universe. Even now, many scientists are theists.
And secondly, the reason God is ruled out as a reason for things almost a priori, is because that hypothesis has been wrong in every other thing we have ever figured out... ever.
We know how planets form themselves.
We know how galaxies form themselves.
We know how the universe came to look the way it does.
We know how weather works.
We know how bacteria/viruses/disease/pestilence works.
We know how earthquakes/tornadoes/hurricanes/floods/volcanoes work.
We know how evolution works.
These are all things that God used to be the hypothesis for, and it turns out none of them have anything to do with him. So why would we make a guess that God did it now when that guess has been wrong every time before?
Again, no serious apologist believes in a god of the gaps. That's just a caricature that atheists throw out. Christians believe, just like the early scientists did, that God works through nature. It's called providence. If you're looking for empirical proof for the existence of God, you should study the evidence surrounding the Resurrection.
Here's a site for that...
http://www.reasonablefaith.org/the-resurrection-of-jesus
...although some other scholars have done even more in-depth studies.
Here's another link:
http://christianity.about.com/od/easter/a/7-Proofs-Of-The-Resurrection.htm