a difficulty with Nietzsche

The most common problem seems to be a gross misunderstanding and oversimplification. I've heard evangelical christians say (and paint on walls) the expressions

"God is Dead" -Nietzsche
"Nietzsche is Dead" -God

A better reading, but still a simplification is

"the idea of God is no longer capable of acting as a source of any moral code or teleology" (wikipedia)

In this light many Christian apologists should see Nietzsche as their ally rather than their enemy. The main point of agreement here is that Christianity was the source for morality in the past. A lot of contemporary atheists would deny that Christianity was ever a necessary source for morality and that it never in fact provided much (they probably go on to list the many crimes committed in the name of Christianity over the years).

My difficulty arises in that point of agreement. I think Nietzsche is saying that science has basically produced this set of affairs, that we're now incapable of seeing God (or "any idealogical philosophical system" -wikipedia) in adequately meaningful ways (practically) because science has provided other explanations. I tend to see human nature in terms of

That which has been is that which will be,
And that which has been done is that which will be done.
So there is nothing new under the sun.

Ecclesiastes 1:9

From a more "natural science" point of view I don't think evolution works quickly enough that we can see it happening (the basic nature of man doesn't change over shorter time periods -- even thousands of years). Looking at other cultures and their structure too steers me away from this linear progression way of thinking. Along with that you have to see positive progress to see negative progress, I don't see either, at least not in human nature.

The difficulty is then that I think Nietzsche sees what I see (and further and deeper from many an aphorism) but then I probably don't understand his view at all. What am I missing?

At the moment I don't think there is much that is a response to Nietzsche but only a response to this or that particular strand and how that has been interpreted. I'm almost always in agreement with one side of what he thinks but the other sides creep up and it's hard and probably not good to simplify/systematize.