This is pure speculation, but my guess is that signal spec licensing sits on shaky legal ground and that the big manufacturers are more than happy to pay up to avoid fighting a lawsuit that they may or may not win. Similarly, those that own the IP for the HDMI spec are unwilling to sue a small fish like the Raspberry Pi foundation, because even if they win, there's not much money to be made. And if they lose, then Samsung and Apple and Dell will realize they don't have to pay anymore, which
would amount to a lot of money.
DisplayPort is a free spec and can be easily converted to HDMI, so I don't really understand why anyone uses HDMI. HDMI has more bullet points but I've never seen a device that can do anything more than deal with audio and video through the same cable. And Display Port does that fine.