Atheists tend not to be that interested in theology — we're typically more interested in apologetics — but we do have something to say about theology itself.
The most common atheist critique of theology is that the literal meaning of the Abrahamic scriptures (Torah/Old Testament, New Testament and Koran) is rather disgusting from a modern ethical viewpoint (not to mention completely nonsensical from a modern scientific viewpoint). The Old Testament is a dead loss, exhorting the death penalty for just about everything, approving murder, incest, genocide, aggressive wars of conquest, human sacrifice, slavery and rape. The New Testament is a little nicer, but still explicitly condones slavery, establishes the inferiority of women and condemns homosexuality. It's also strongly sex-negative in general, and sexuality is an important and integral part of the human experience. The Koran is explicitly theocratic, anti-democratic, misogynist, and explicitly relegates infidels to second-class status. And of course the New Testament and the Koran establish the idea of eternal torture in hell, by definition the most immoral — by humanist standards — idea it is possible to promulgate.
Of course, the conclusions above follow from a fairly literal reading of the scriptures. Some theologians, however, hold that the literal reading is unjustified; that modern theology takes a more nuanced and subtle approach, and escapes such criticism. This defense, however, fails miserably.
There are, of course, tens or hundreds of millions, perhaps billions, of people who do indeed read their scriptures literally. It is ridiculous to assert that some criticism is specious just because the writer himself is not in the category being criticized. I might as well argue that criticism of Nazism is specious because I myself am not a Nazi. Indeed if I made such an argument, one might justifiably be suspicious that I had an ulterior motive for shielding Nazis from criticism.
But "liberal" non-literal theology also deserves criticism on its own merits.
First, liberal theology is very hard to read; it's mostly ambiguous and vague, awash in bullshit. It's a struggle just to find a simple, unambiguous declarative sentence... much less a whole paragraph that makes sense. An example trotted out by the liberal theologians is Tillich's notion of God as not a being but "Being itself" or the ground of all being. This idea is simply nonsense, a profound-sounding hook on which to hang a bunch of mystical mumbo-jumbo. Liberal theology is just another instance of mystical Deepak Chopra-style woo-woo. But it's woo-woo with a bite.
A fundamental problem with liberal theology is its methodology. It's all well and good to argue that the literal interpretation of a text might not be the best interpretation. I doubt anyone would argue that, "My lover is like a gazelle or a young stag," should mean that the lover has four legs and fur. On the other hand, the literal interpretation is always the facially simplest explanation; it requires a positive argument to establish an alternative.
The liberal theological methodology, however, seems to be that if the conclusion drawn from the literal meaning is objectionable, then the text is "metaphorical". If you can't find a plausible metaphor to rescue the text, then the text is "mysterious". The text always means what the interpreter wants it to mean, and if it can't mean that, then it means nothing. The truth or the correct moral opinion is formed externally, and then used as an interpretive schema.
There's no problem with determining the truth or ascertaining acceptable moral belief outside some scripture. The problem is trying to mangle a modern conception of scientific and ethical belief into the procrustean bed of iron age mythology created by barbarians who were, by modern standards, quite nasty people. Not their fault, they didn't know any better, and they deserve our pity more than our scorn, but they were what they were: nasty, superstitious, slave-owning, violent, murderous, xenophobic, war-mongering, woman-hating savages.
Why go to all the trouble of trying to interpret savages' mythology in light of modern science and ethics? Why not just say what you think is true and good and abandon the attempt to reinterpret ancient superstitions?
Nobody writes or speaks only because he loves the sound of his own voice. If that were the only motivation, he'd just sing in the shower. Everyone writes because he wants to be believed, to be taken seriously, to communicate — to communicate at least that he is an especially clever and profound fellow who deserves a six-figure tenured sinecure at a major university.
One of the easiest ways to be believed, to be taken seriously, is to piggy-back on some authority. It's not enough to say that Being itself or the ground of all being is an important philosophical concept; Tillich says that the Christian God is the ground of all being, and thus the concept is philosophically important. But to piggy-back on an authority is to lend credence to that authority and, more importantly, to lend credence to the general idea of ideological authoritarianism. So, by seeking to reinterpret scripture in light of modern science and ethics, the liberal theologians are reinforcing the authority of scripture.
The liberal theological methodology works both ways: If you're an authoritarian submissive, if you're neurotic and hung-up about sex, if women scare the shit out of you and fags creep you out, if you think black and brown people are dirty and stupid — and if the text means what you want it to mean — then your interpretation is just as valid as any liberal theologian's. And these ideas are generally well-supported by a literal interpretation of most scriptures; the scriptures unsurprisingly tend to reflect the atavistic prejudices present at the time of their writing.
Furthermore, because there is often no reason other than the objection to the conclusion to force a reinterpretation of the text, those who argue for a literal interpretation have a stronger case. Indeed if the notion of scriptural authority is to have any meaning, then by definition objecting to the literal conclusion is not a valid rebuttal. Just that I don't like the law is not an argument that the law does not in fact prohibit, for example, the possession of marijuana. Dislike might be an argument to change the law, but it's not a good argument to reinterpret the law away.
And that's the "bite" of liberal theology, and why liberal theologians must protect their literal, fundamentalist, extremist brethren at any cost in honesty, integrity and common sense.
The atheist critique of religion in general does not seek to undermine the literary value of scripture, its historical or sociological importance nor even its "spiritual" value. The atheist critique of religion seeks to undermine the authority of scripture, and an attack on the authority underlying the extremists' and fundamentalists' views is just as much an attack on the authority underlying the liberals' views.