Bungie addresses this in their own FAQ but is a tiny bit ambiguous. The announcement press release seems to indicate yes; their FAQ equivocates, saying that Halo 3 concludes the current story arc (pun most likely intended; looks like Bungie finally hired Stuntmutt).
There is every indication that Bungie has been undergoing fatigue over the Halo franchise since crunch time on Halo 2, and I would be very surprised if Bungie did not want to work on something entirely different after Halo 3, or if indeed Bungie has a second team quietly working on something else right now.
However, from Microsoft's perspective, the Halo franchise is the engine that drives Xbox and Xbox 360 sales. There would seem to be no guarantee that whatever Bungie wants to work on next will be as sure-fire a seller as the Halo games have been to date.
Bungie may be hedging its answers by specifying the "current story arc" is ending because it seems possible, if not downright likely, that after Bungie finishes with Halo 3, Microsoft might choose to have another studio work on the franchise, either in shooters or another genre. Rumors have circulated to this effect since Halo 2 was in development; Halo universe RTS games, Halo universe MMO games, etc.
Source: Bungie Halo 3 trailer FAQ
UPDATE: Since this entry was written, Ensemble Studios has unveiled their Halo Wars RTS for the Xbox 360, and Wingnut Interactive has announced its intention to make some form of interactive digital entertainment product set in the Halo universe. The most complete answer to this question is that the story we've been following in Halo 1 and 2 is coming to an end in Halo 3, but that other developers will be carrying on with other products in the Halo universe. What Bungie's plans are post-Halo 3, nobody else knows yet.
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