As I think I've mentioned before, I knew one of Trump's senior advisors, John Kelly, very well. It is easy to see why they would have gotten along well at first, and also why it would have fallen apart.
Kelly is a very smart, very well-read, and disciplined guy. All-business, and I imagine that appealed to Trump. Trump liked him a lot as Homeland Security.
As Chief of Staff, the way they each approached their jobs was bound to clash at some point.