You missed out the fact that not only had the previous Captain of the Beagle committed suicide, but so had an uncle of Fitzroy's - Castlereagh. Fitzroy employed Darwin not, initially, as the Beagle's naturalist, but as a companion for himself to keep him sane. He thought madness could be in his blood.

However, Darwin and Fitzroy argued during the voyage - slavery was part of that argument - and at one point Darwin was actually banished from the Captain's table.

Fitzroy was a deeply religious man, and when Darwin did eventually publish his theories Fitzroy was appalled to learn that Darwin had begun developing them whilst aboard the Beagle. Fitzroy spoke out against Darwin to anyone who would listen and eventually, so tormented was he by what he felt he had done to the Church, he killed himself!