I think it's most likely a combination of a bunch of things, like that Axios article says. Basically:
1. Keep Trump and rookies/neophytes from doing anything too stupid.
2. Reluctance to abandon colleagues such as Mattis.
3. Trump isn't that bad in person, face-to-face.
4. We like the power.
For each person that ranking of priorities is probably different, and there might be one or two pet-projects that are on each person's radar, but I could see myself in that situation. How many of us have stuck around at a terrible job with a terrible company because the people we work with day-to-day need us? That alone is a powerful motivator.
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