By getting you to spend more time in their interface, they can add things. E.g. Prime Music had me spending a lot of time checking out playlists, some of which may very well lead to purchases of albums where only a couple of songs are available for free.
It also gets them penetration for whenever they add shopping to these devices, and e.g. lets you talk to Echo and ask it to bring up the top five best new phones on your TV for you to choose fro.
Getting Prime on Chromecast would help their penetration of Prime, but it might hinder their overall service penetration by giving some people a reason not to get a Fire Stick. Especially when the Fire Stick/Fire TV and Chromecast are all cheap enough that there's little stopping people from getting both...
It may very well backfire for them, but there's all kinds of reasons for them to want to push the Fire TV devices hard.
I don't have enough ports on my TV for a Fire Stick and a Chromecast (and everything else) so I'm going to choose the one with the most options (Chromecast).
They can lose a lot of users and still find it to be worth it for the extra engagement of the ones they did get.
Amazon makes some strange decisions.