What's interesting is how complex Zarek actually is as a character. He's greedy and power-grabbing, but at the same time actually does believe in what he's preaching.
For instance, allowing ship captain's to decide if Cylons were allowed aboard their ships completely undermines his federal authority and sets up a precedent for a more balkanized fleet political structure. Yet, it seems like he did this because he honestly did feel that it belonged in the hands of the ships. (of course he's done enough wheeling and dealing that this change of policy wouldn't hurt his own personal power...)