I am trying to use Bankful for my subscriptions, but it says that I am not eligible for auto-charging subscriptions

To use Bankful for your auto-charging subscriptions, make sure that you connect the new, native integration of Bankful into your Shopify account and not the older, hosted version. 

This native integration of Bankful into Shopify will allow you to accept auto-charging subscriptions in your shop.

Read more about this here: https://support.bankful.com/shopify-native