Science can tell you an awful lot about contingent oughts ("in order to achieve X you ought to do Y"), and it's not completely clear that non-contingent oughts even exist. (We like to think they do since it saves arguing about whether X is worth achieving, which ends up with the realization that we don't have a satisfyingly solid grounding for knowledge, etc..)
Unfortunately, Sam Harris doesn't really delve into the issue adequately; rather than making a spirited defense of the value of contingent oughts like e.g. Daniel Dennett does, he just expresses his feeling that of course science can tell you what you ought to do. (And not in a very impressive way, either--he starts with really clear cases where everyone agrees what to do and notes that adding a scientific perspective doesn't change anything, and then as far as I can tell dismisses the rest as details.)
Instead, it would have been nice if he had brought to bear the full force of contingency, including extinction if you screw up too badly. Harris' personal views seem to be very typically American--highly individualistic and happiness-based, in particular--which may explain in part why he didn't go in that direction. Happiness is great and all, and it's nice not to worry about people telling you what to do. But when one starts from "we're intelligent social primates in an indifferent and largely deadly universe", it's hard to get to a point where you don't start thinking it could potentially be a good idea to curtail individual freedoms to maintain environmental sanity, and that we should probably demand a much higher degree of attention to nurturing our offspring to enable them to make informed decisions about this complicated technological society we've built.
(Someone needs to write a book titled "Your Feelings are Trying to Make You Evolutionarily Fit in a Social Context".)
Anyway, I view the is/ought divide as probably much ado about nothing; I think when we end up fully exploring the force of contingent oughts, we may have enough. (In a way similar to coherentist views of knowledge--you can't perfectly ground things, but when everything you care about ties together, that's good enough.)