Even if, as seems likely, Musharraf is totally against al-Qaeda, and would try to eliminate its sympathizers from his government, there were other sources of plots to kill Bhutto--and he no doubt was well aware she was the most likely person to take his position. So he may not have wanted to devote many resources to protecting her. His answer would no doubt be that he did not have the resources, and that keeping her under house arrest was protecting her. (With the added, unsaid, side benefit of preventing her from effective campaigning).

But at this point this is straying into the realm of pointless speculation.