I've seen a fair number of talks and debates featuring Sam Harris. Out of the contemporary secularist popular philosophers, he is my favorite. Though Christopher Hitchens was fun as well and deserves a mention.
I generally agree with him that morality is not purely subjective, and I've actually used some of his arguments on that point before. I tend to think that even if you take a naturalistic and empirical approach, it is fairly clear that morality is not something that we just made up and that it is not purely dependent on our minds.
I also agree with him that science can help us answer moral questions so long as we have established a naturalistic definition of moral good beforehand. Of course, this simply means that the question remains, what is moral good? His answer has to do with the prevention of suffering because of the commonality of concern with human suffering on the part of other humans. I do not see suffering as a moral evil (probably a controversial position), and so I'm obviously not going to agree with his conception of morality or the implications of it.
I think that positioning the prevention of human suffering as the basis of morality because of its commonality is to collapse the is-ought distinction and that the result is a meta-moral or meta-ethical claim rather than a moral or ethical claim. In short, he isn't proposing an objective moral standard at all, but rather a description of how we often make moral decisions. He is suggesting that the IS is also the OUGHT, which is not so much a valid criticism of the is-ought (or fact-value) distinction as it is an a priori rejection of it. It is indeed begging the very question at issue in his argument, the question of whether or not values are reducible to facts.
Let's leave that aside for the moment and say for the sake of discussion that he's correct in his view that the objective basis for morality is the prevention of suffering and that science can help us answer the questions related to how we prevent suffering and foster "human flourishing".
If he is correct, then science not only has an epistemology, an ontology, a creation narrative, an eschatology, a clergy, and predictions; it now has a morality. This means that science is able to provide us with all the critical functions of a religion. For many secularists, this would be uncritically viewed as a great victory. After all, what could be better than to have something which could perform all the positive functions of religions without being a religion?
But let us consider for a moment why we would think of science as something other than a religion at this point. If a thing performs all the same basic functions as another thing, what is the difference between them?
Perhaps we could make the distinction by saying that science, while it has made a fair number of wrong predictions, has made more right predictions than traditional religions. Well, alright. Even if we notice that a Linux server runs faster and has fewer problems than a Windows server, do we say that the Linux server is not a server at all?
Of course not. It is still a server because it performs the same basic functions.
Perhaps we could make the distinction by pointing out that science leads to working technologies far more often than traditional religions, that it provides a better basis for engineering. Do we say that the Arlington memorial bridge is not a memorial at all because it serves a practical purpose more effectively than most memorials?
Of course not. It is still a memorial because it has the function of a memorial.
In the end, if his view is correct, then science is a full-fledged religion, right down to having its views privileged in our educational system. And because at this point science is a religion, he is not really opposed to religion at all.
He's just opposed to religions other than his own and wants to privilege his religion above all others by persuading the uneducated masses to his view. Which means that he is a religious demagogue in his own right. I rather doubt that he would want to be a religious demagogue, and I think that the consequences of his view would be particularly abhorrent to his fellow secularists who have a rather dim view of religions.
He might be better off upholding the is-ought or fact-value distinction. As someone who really likes science and appreciates the immense value of it, I am incredibly disturbed by the idea that we should take the final step toward making it a religion, and I would suggest that we need to very carefully consider the consequences of doing so.
Surveying the Moral Landscape - Surveying the Moral Landscape Again
Note: The above is a picture I took while running alongside a river.