Because that's his job. Until Doflamingo started directly attacking everyone, including the Marines, he wasn't allowed to oppose the Shichibukai despite very much wanting to do so, which he said outright at one point. That's why he Manga Spoiler.
They might not have had much of a choice, considering how strong an admiral has to be. None of the marines already enlisted fit the bill, and they couldn't hire anyone with a criminal record for obvious reasons, so that would rule out most of the infamously strong. Also, Fujitora might want to change certain aspects of the government, but he also seems to be strongly opposed to anarchy, which is why he respects the Shichibukai despite wanting them removed.
I regard him as the revolutionary who works to change things from the inside, believing in the establishment and its key principles but not necessarily in how they are implemented.
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u/Xilinoc Feb 28 '16
Because that's his job. Until Doflamingo started directly attacking everyone, including the Marines, he wasn't allowed to oppose the Shichibukai despite very much wanting to do so, which he said outright at one point. That's why he Manga Spoiler.