'Cause the reality is that majority of people aren't fit to be parents.
I've had something like 6 chances to have a decent paternal figure in my life and they have all been dogshit lol in my 33 years of living I've only met a handful of people who had parents worth a damn.
A lot of these mangaka/authors are also writing from personal experience or using lived experiences of people they know. So, if there are a lot of stories that have shit parents in them it stands to reason that maybe there are just a lot of shit parents in the world.
You also have to realize that to be an artist you also have to be a lil fucked up in the head.
Sincerely,
An artist who is severely fucked in the head lol

Granted, this one's rather unique--ML's mom left the family, ML's dad threw himself into his work, ML tried to copy his dad to get his affections and ended up surpassing him and making him resentful, and his dad passed away. I know communication isn't the strongest thing for parenting style in a lot of cultures, but this is rather sad for no reason. IDK why we had to have a "your dad despised you until he died" storyline instead of something happy. Why is it so rare to have a BL with non-toxic dads?