As I noted on Twitter earlier, I think this bold move certainly has the prospect of backfiring. For one, it falls into the trap of reinforcing or reigniting the Muslim rumors from the campaign (even if without justification). As his first interview as President, it does seem like odd timing - why not hold off a week or two at least? Why not slip in an American interview first?
On the other hand, as one roommate hypothesized, he needed to do it now while he still has the political capital to do it under the mantle of a mandate (I responded that the move's timing will most certainly contribute to a diminution of political capital at home). The timing does send a strong message to the Arab world. While it didn't run first in the New York Times today, I think, in the long run, it will be seen as the most historic bit of news from today. In a way, I see Obama pushing toward a "Nixon Goes to China" move that marries his unique personal positioning to a pressing U.S. foreign policy problem. He's looking to toss out a game changer with parties in the region while appealing to his base back home by taking a wholly different approach than Bush.
But on the whole, that will take time to sink in. In the immediate future, it's probably more problematic on the domestic front. I also disagree with Obama's belief that the U.S. can make meaningful headway in resolving the eternal Arab-Israeli problem by involving itself.