Justice Oliver Wendell Holmes is supposed to have said (something like) "I don't know what obscenity is, but I can recognize it when I see it." And therein lies the problem.
You are exactly right - pornography is allowed to flourish under the banner of free speech, but art is stifled in the interest of protecting the innocent. Whining about the problem won't lead to a solution. What is needed is constructive discussion leading to a clear, objective, universally accepted definition of the line that separates art from pornography. The challenge, of course, is that the factors that tend to make pornography obscene are often in the motivation of the maker and, of greater concern, in the interpretation applied to the work by the viewer.
In my opinion, art becomes pornography when the maker chooses to employ elements that intentionally titillate the viewer. Your photograph of a partially-clothed child, like Sally Mann's photographs of her children, were intended to document normal times in the lives of these children. There's nothing pornographic in normal childhood, and you certainly weren't targeting pedophiles as the market for your photographs.
But that's where the viewer's interpretation comes in, and where things get really sticky. My wife understands and appreciates art, and she accepts, intellectually at least, that nudity can be part of art. And yet she is very uncomfortable with nudity at any time or any place, and tends to view images that involve nudity as somehow perverse.
I think part of the problem comes from the fact that photography is unique among the visual arts in that it is democratic - anyone can do it (sort of). Most people view photography as a means of recording pleasant and memorable events - birthdays, holidays, etc. As a result, those people have an instantaneous reaction to photographs of thinking in terms of the event that was photographed rather than the photograph as an exercise in art. Therefore, when the see a photograph that involves nudity, their immediate reaction is to ask what was happening at the time the photograph was made. They attempt to read into the image actions that may or may not have occurred. My suspicion is that a lot of the problem that we as photographers have is that viewers are reading actions into our images that took place only in their own minds. In others words, the problem is not that we make dirty pictures, but rather that some viewers have dirty minds.
But I don't think that's necessarily the whole story. I know my wife doesn't have a 'dirty mind', but she still reacts negatively to images involving nudity. She (and I) both grew up in atmospheres in which nudity was not 'normal'. I can't speak for her childhood since I wasn't there, but I know that in my case, I was never explicitly told that nudity was wrong - it simply wasn't done. We learn a lot by example. I suspect that those who grow up in an atmosphere in which nudity is more common are far more willing to accept nudity in art.
So I don't think this is a problem that can be solved quickly. We can have a discussion about pornography and art, but it is going to be difficult to reach agreement on where the boundary lies.