Super-reporter Spencer Ackerman gets Bhutto’s close friend and confidante Husain Haqqani on the record thusly:

The whole Pakistani security establishment thinks Pakistan should be governed as a national-security state. She resisted that completely, and that doesn’t get seen enough. She questioned their right to govern.

There’s the crux of it. Look no further.

I hasten to add, without condoning the assassination in any way, that it’s quite possible that they’re correct and she was not.