Okita was placed in Kondo's care as a small child and as far as I can tell Kondo never taught him much other than how to fight. I don't think Kondo had much interest in caring for the emotional needs of a traumatized child. When we meet him, Okita sees himself as Kondo's tool. Kondo strikes me as a fairly selfish person and I wonder if Kondo valued Okita as anything other than a tool.

Having said that, there are definitely more positive readings of the relationship in the fandom, and I've seen a lot of fics in which Kondo is great with young!Okita. You could also make the case that none of this was Kondo's responsibility, he didn't ask to be a dad.