Here is my take. First I don't think naive realism is a pejorative term although I do understand why it would be taken as such. I think naive realism is the basic outlook of most people. So I don't see it as an unreasonable or stupid attitude but I guess 'naive' does carry negative connotations.
Now what does 'naive realism' contrast with? Scientific realism would be one. A 'scientific realist' might say that the universe is not anything like what humans perceive, it is 'really' completely alien to anything we can imagine and full of invisible entities like neutrinos, the zero-point field, dark matter, and so on. But s/he would still feel that these phenomena would be real
phenomena and the subject of scientific investigation - so a realist, but not a naive realist.
But I think the whole 'realist' perspective - whether naive or sophisticated - has been called into question by developments in science itself.
First is the interpretation of quantum mechanics, where many of these debates about realism have originated. As is generally known, the so-called Copenhagen Interpretation of QM raises the question of the extent to which matter at the most basic level can be understood as existing separately from an observing intelligence.
Second is in 'cognitive constructionism', which demonstrates that our sense of 'what is real' is very much an artifact of our frontal lobes and central nervous system and our 'embodied cognition'.
I don't want to re-open these debates here as they are perennial topics in other threads, but it might help to recall the context within which the question often arises.
I think, then, that question of realism comes up in the discussion of objectivism, or the sense of 'mind-independent reality'. Many seem to take it for granted that this is 'what is really there'.
But surely this is the basic outlook of the natural sciences? I mean, the whole move away from metaphysics in Western thought, was an attempt to ditch the endless metaphysical debates and scholasticism and study 'what was really there'. This was very much the underlying motivation of Hobbes, Bacon, Galileo, Descartes, and many of the founding fathers of our modern worldview, whether scientists or philosopher. Whether their specific outlook amounted to naive realism, representational realism, or scientific realism, I am sure that all of these thinkers could be broadly characterised as realists and their chief concern was with 'natural philosophy' rather than what they called (with good reason) speculative metaphysics.
So where I am going with this is that I think science itself has started to undermine the realist outlook. I think this is why working physicists generally avoid philosophical debate, because it is has been clear since QM was discovered that generally speaking the realist or naturalist account of matter has been seriously undermined. Hence the interest in Eastern philosophy - scientists are 'fishing for a metaphysic' to make sense of the anomalies and absurdities thrown up by QM. This is why Einstein was so troubled by QM - it threatened what he saw as the basic scientific outlook of naturalism. Which I am sure it does.
That is my take on the debate.
---------- Post added 03-12-2010 at 04:00 PM ----------
I think this leads to some kind of platonist or transcendental realism, where 'what is really there' is an intelligible structure rather than an object, per se. I think, although I haven't read much about him, Roger Penrose supports this kind of outlook.