WooCommerce Payments will support charging automatic recurring payments via the WooCommerce Subscriptions plugin in a future version. For now, it can only be used with manual recurring payments.
If you would like to use WooCommerce Payments to sell subscriptions with automatic recurring payments, please vote for the Idea on our Ideas board. The popularity of an Idea influences the priority in which that feature is implemented. The more votes the Subscriptions Support idea gets, the sooner it will be implemented.