Yup. When I receive donations through Ko-fi (which also goes through Stripe), then Stripe take a percentage.

However, when some sites use either paypal or Stripe to pay earnings, then the site (like Medium or Hubpages) bear the cost.

I don't know what that cost is, but let's say that Medium has to pay $1 for every payment they make, and the writer only earns $0.50 per month, that is a loss for Medium.

I think that is why they did it. :)