New Atheists and religious fundamentalists share a view of both God and religion that is unhistorical, simplistic and essentially Medieval in outlook.
One of the most common complaints made by liberal and moderate believers is that atheist critics are focused on versions of theism and religion which are too "simplistic" to be legitimate. Atheists are ignoring "sophisticated" versions of theism and religion which happen to be immune to atheists' arguments. At best atheists are therefore just theologically illiterate; at worst they are targeting a straw man in order to make a weak position look stronger. Is this a fair objection?
Real vs. Fake Straw Men
Dismissing or criticizing someone's critique of a concept on the basis that they have offered only a simplistic view of that concept can be legitimate. At best it may be that the original critic simply doesn't correctly understand the concept they are criticizing; at worst, they may in fact be deliberately using a straw man to make their criticism easier. Atheists offer this sort of response to religious theists quite often; for example we dismiss creationists' attacks on evolution because they have such a simplistic idea of evolution.
Even if it is true that one is focusing on a relatively "simple" version of a concept, though, this doesn't necessarily invalidate their criticism of that concept. Criticism of a simplistic version of a concept is a problem when the simplified version does not accurately reflect how that concept is generally understood and used. Creationists' simplistic understanding of evolution invalidates their criticism, for example, because they aren't criticizing evolution as working evolutionary biologists actually use the concept in their research. Thus even if their arguments are sound, there are no negative consequence for evolutionary theory or evolutionary biology.
Critiquing Popular Religion
So if atheists' criticism of theism and religion is invalidated because they are using simplistic concepts of god and religion, it can only be because they are not using concepts of god and religion as they genuinely exist among theists and religious believers. Given how varied religion and theism can be, it would be difficult to criticize a form of religion or theism that doesn't exist somewhere, so to be most fair to believers, we should stipulate that it must be the case that atheists are not using concepts of god and religion which are common, and preferably predominate, among theists and religious believers. Is that the case?
Absolutely not. First, no matter how "simplistic" the concepts of god and religion criticized by atheists may be, these are the sorts of concepts actively used by large numbers of religious believers generally and Christians in particular, at least in the United States. Even if it were to be conceded that more "sophisticated" versions of these concepts exist (and that's not clearly the case, because more complicated language and metaphors doesn't render a concept "sophisticated") they shouldn't be atheists' primary target of criticism if they are only actively used by a relative minority of believers.
Second, critiques of a simplistic form of an argument or position can still have serious implications for more sophisticated forms of that argument or position. For example, if a critique focuses on problematic premises that are key to that position, and the "sophisticated" forms rely upon those premises in the same way as the simplistic forms, then the critique applies to both. Defenders of the sophisticated form would need to demonstrate that their version recognizes this weakness and incorporates solutions; otherwise, their objection to the critique is baseless.
Religious Apologists' True Colors
If liberal and moderate believers think that they have a legitimate case for the idea that atheists are only criticizing inappropriately simplistic versions of gods and religion, then they need to demonstrate that more sophisticated versions of those concepts are much more popular and common than the "simplistic" ones which "new atheists and religious fundamentalists" focus on. If this were a true state of affairs, ten it shouldn't be too difficult to demonstrate because there have been so many surveys done about religious beliefs in America over the years.
It should be possible to pick out a few characteristics of the "simplistic" concepts and see just how popular they are in America relative to more "sophisticated" characteristics. If the liberals and moderates are right, the empirical data should be there — and atheists should accept that they need to redirect their focus to the more common concepts out there. It does us no good to criticize theism or religion if we spend all our time on forms which aren't very common.
On the other hand, if the data demonstrates that atheists are indeed criticizing the more popular concepts, then liberals and moderates need to admit that atheists' criticisms are not focused on an inappropriate target — and they should admit this just as publicly and as strongly as they have been when attack atheists in recent years. That would be the fair and decent thing to do; then again, the fair and decent thing to do would be to locate data supporting their accusations in the first place.
The fact that liberals and moderate persist in these accusations without the benefit of supporting evidence, and despite the presence of strong contradictory evidence, suggests that they aren't interested in being fair or decent at all. This is one reason why it's reasonable to suggest that liberal and moderate believers end up providing cover for fundamentalists and extremists, even if inadvertently. Religious believers who are more upset over the appropriate criticisms from outsiders than the inappropriate behavior and beliefs of fellow adherents are showing their true colors.