The inevitable question after any assassination is: who benefited from it? The answer in this case is Musharraf and the extremists. Bhutto was the enemy of both. Could they have worked together to eliminate her?
With her murder Musharraf has had his chief rival removed and he can resume his authoritarian rule with the Americans off his back: Washington has nowhere else to turn. He is the man. He has secured power--for the time being anyway. Musharraf has played America brilliantly. His intelligence service helped create and still has ties to al-Qaeda and the Taliban. Indeed, Bhutto accused him of harboring extremists for just such an attack. Their claim of responsibility gives Musharraf deniability, since he is supposed to be fighting them.
Now Musharraf can clamp down on the human rights and democracy crowd, his real enemy, while running his phony war against extremists, all the while taking American military aid intended to fight terrorism and use it to upgrade his defenses against India. A very clever, but dastardly plan.
If Musharraf's claims are to be believed, then rogue elements of his intelligence service were involved in the killing and not Musharraf himself. But the effect is the same: he is not effectively fighting the terrorists and he benefits from their enmity with democracy and from American financial backing.
But Musharraf's game is dangerous. For the moment, the Taliban and al-Qaeda won't touch him, because he has their back, as it were. He is an uneasy ally for now, keeping the gullible Americans, or at least American public, believing he is actually fighting them.
Musharraf must fear that this game will last only until al-Qaeda and the Taliban feel strong enough to try to overthrow him and rule Pakistan with their allies in military intelligence. That day hopefully may never come. But in the meantime he is a very useful placeholder for them.